From 6212dd60e4e7963397f67c5256f7d9963ddce4b9 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Fri, 30 Jan 2026 09:49:39 -0600
Subject: [PATCH 1/3] Update vcfpy dependency to a newer version and update
 test data

---
 setup.py                                      |   2 +-
 .../af_number_1.bam-readcount.readcount.vcf   | 153 ++++++++++++++++++
 tests/test_data/existing_sample.genotype.vcf  |   2 +-
 tests/test_data/hom_ref.readcount.vcf         |   2 +-
 tests/test_data/indel_mode.bam_readcount.vcf  |   8 +-
 tests/test_data/info2_output.vcf              |   2 +-
 tests/test_data/info3_output.vcf              |   2 +-
 tests/test_data/info_annotation.vcf           |   2 +-
 tests/test_data/input.cufflinks.gx.vcf        |   2 +-
 tests/test_data/input.cufflinks.tx.vcf        |   2 +-
 tests/test_data/input.kallisto.gx.vcf         |   2 +-
 tests/test_data/input.kallisto.tx.vcf         |   2 +-
 .../input.kallisto.with_version.tx.vcf        |   2 +-
 tests/test_data/input.stringtie.gx.vcf        |   2 +-
 tests/test_data/input.stringtie.tx.vcf        |   2 +-
 tests/test_data/multiple_samples.gx.vcf       |   2 +-
 .../test_data/multiple_samples.readcount.vcf  |   2 +-
 .../multiple_samples_second_alt.readcount.vcf |   2 +-
 tests/test_data/multiple_transcripts.gx.vcf   |   2 +-
 ...ltiple_transcripts_one_missing_gene.gx.vcf |   2 +-
 tests/test_data/no_gt_in_format.genotype.vcf  |   2 +-
 .../no_matching_readcount.readcount.vcf       |   2 +-
 .../output.hard.filtered.vcf                  |   0
 .../output.no_protein_pos.filtered.vcf        |   2 +-
 .../test_data/single_sample.dna.readcount.vcf |   2 +-
 tests/test_data/single_sample.genotype.vcf    |   2 +-
 .../test_data/single_sample.rna.readcount.vcf |   2 +-
 ...isting_readcount_annotations.readcount.vcf |   2 +-
 tests/test_data/snv_mode.bam_readcount.vcf    |   8 +-
 .../test_ref_transcript_mismatch_reporter.py  |  28 ++++
 tests/test_vcf_expression_annotator.py        |  70 +++++++-
 tests/test_vcf_genotype_annotator.py          |  25 ++-
 tests/test_vcf_info_annotator.py              |  25 ++-
 tests/test_vcf_readcount_annotator.py         | 145 +++++++++++++++--
 34 files changed, 462 insertions(+), 50 deletions(-)
 create mode 100644 tests/test_data/af_number_1.bam-readcount.readcount.vcf
 mode change 100755 => 100644 tests/test_data/ref_transcript_mismatch_reporter/output.hard.filtered.vcf

diff --git a/setup.py b/setup.py
index 5fabd99..b5a6391 100644
--- a/setup.py
+++ b/setup.py
@@ -16,7 +16,7 @@
         ]
     },
     install_requires=[
-        'vcfpy==0.12.3',
+        'vcfpy==0.13.8',
         'pysam',
         'pandas',
         'gtfparse==1.3.0',
diff --git a/tests/test_data/af_number_1.bam-readcount.readcount.vcf b/tests/test_data/af_number_1.bam-readcount.readcount.vcf
new file mode 100644
index 0000000..c3ecd0a
--- /dev/null
+++ b/tests/test_data/af_number_1.bam-readcount.readcount.vcf
@@ -0,0 +1,153 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=BCNoise,Description="Average fraction of filtered basecalls within 50 bases of the indel exceeds 0.3">
+##FILTER=<ID=DETP20,Description="Average distance of the variant base to the effective 3' end is less than 0.2">
+##FILTER=<ID=IRC,Description="Unable to grab any sort of readcount for either the reference or the variant allele">
+##FILTER=<ID=LowEVS,Description="Somatic Empirical Variant Score (SomaticEVS) is less than 20">
+##FILTER=<ID=LowQual,Description="Low quality">
+##FILTER=<ID=MMQS100,Description="The average mismatch quality sum of reads supporting the variant is greater than 100">
+##FILTER=<ID=MMQSD50,Description="Difference in average mismatch quality sum between variant and reference supporting reads is greater than 50">
+##FILTER=<ID=MQD30,Description="Difference in average mapping quality sum between variant and reference supporting reads is greater than 30">
+##FILTER=<ID=MVC4,Description="Less than 4 high quality reads support the variant">
+##FILTER=<ID=MVF10,Description="Variant allele frequency is less than 0.1">
+##FILTER=<ID=MVF5,Description="Variant allele frequency is less than 0.05">
+##FILTER=<ID=NRC,Description="Unable to grab readcounts for variant allele">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=PB10,Description="Average position on read less than 0.1 fraction of the relative distance from the read start or read end">
+##FILTER=<ID=QSI_ref,Description="Normal sample is not homozygous ref or sindel Q-score < 40, ie calls with NT!=ref or QSI_NT < 40">
+##FILTER=<ID=RLD25,Description="Difference in average clipped read length between variant and reference supporting reads is greater than 25">
+##FILTER=<ID=SB1,Description="Reads supporting the variant have less than 0.01 fraction of the reads on one strand, but reference supporting reads are not similarly biased">
+##FILTER=<ID=alt_allele_in_normal,Description="Evidence seen in the normal sample">
+##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
+##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic">
+##FILTER=<ID=homologous_mapping_event,Description="More than three events were observed in the tumor">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FILTER=<ID=multi_event_alt_allele_in_normal,Description="Multiple events observed in tumor and normal">
+##FILTER=<ID=panel_of_normals,Description="Seen in at least 2 samples in the panel of normals">
+##FILTER=<ID=processSomatic,Description="Doesn't overlap a user-input mask">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region">
+##FILTER=<ID=t_lod_fstar,Description="Tumor does not meet likelihood threshold">
+##FILTER=<ID=triallelic_site,Description="Site filtered because more than two alt alleles pass tumor LOD">
+##FORMAT=<ID=ALT_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the alternate allele">
+##FORMAT=<ID=ALT_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the alternate allele">
+##FORMAT=<ID=AU,Number=2,Type=Integer,Description="Number of 'A' alleles used in tiers 1,2">
+##FORMAT=<ID=BCN50,Number=1,Type=Float,Description="Fraction of filtered reads within 50 bases of the indel.">
+##FORMAT=<ID=CU,Number=2,Type=Integer,Description="Number of 'C' alleles used in tiers 1,2">
+##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
+##FORMAT=<ID=FDP,Number=1,Type=Integer,Description="Number of basecalls filtered from original read depth for tier1">
+##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
+##FORMAT=<ID=FOXOG,Number=1,Type=Float,Description="Fraction of alt reads indicating OxoG error">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GU,Number=2,Type=Integer,Description="Number of 'G' alleles used in tiers 1,2">
+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
+##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=QSS,Number=A,Type=Integer,Description="Sum of base quality scores for each allele">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=REF_F1R2,Number=1,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting the reference allele">
+##FORMAT=<ID=REF_F2R1,Number=1,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting the reference allele">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Number of reads with deletions spanning this site at tier1">
+##FORMAT=<ID=SUBDP,Number=1,Type=Integer,Description="Number of reads below tier1 mapping quality threshold aligned across this site">
+##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
+##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
+##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
+##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
+##FORMAT=<ID=TU,Number=2,Type=Integer,Description="Number of 'T' alleles used in tiers 1,2">
+##GATKCommandLine.CombineVariants=<ID=CombineVariants,Version=3.6-0-gf185a75,Date="Tue Sep 04 23:51:04 CDT 2018",Epoch=1536123064627,CommandLineOptions="analysis_type=CombineVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=mutect source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpDHlykf/stgf719f748-5a73-4db3-ae9a-60d5ba7e3608/mutect_filtered.vcf.gz)]), (RodBindingCollection [(RodBinding name=varscan source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpDHlykf/stg3c9d145f-2cdf-4ade-8bbc-244ce4d77fad/varscan_filtered.vcf.gz)]), (RodBindingCollection [(RodBinding name=strelka source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpDHlykf/stg3eae1cb6-aaca-4b53-866f-b5a5d1f83747/strelka_filtered.vcf.gz)]), (RodBindingCollection [(RodBinding name=pindel source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpDHlykf/stge79afa85-e6c4-4b12-b976-6aa58d96a584/pindel_filtered.vcf.gz)]), (RodBindingCollection [(RodBinding name=docm source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpDHlykf/stge47da419-2765-493a-b8f5-ad8f7ff466cb/docm_filter_out.vcf.gz)])] out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdir5BzIoj/combined.vcf.gz genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=mutect,varscan,strelka,pindel,docm printComplexMerges=false filteredAreUncalled=false minimalVCF=false excludeNonVariants=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.6-0-gf185a75,Date="Tue Sep 04 20:31:13 CDT 2018",Epoch=1536111073642,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpi8cINA/stgc022fdc7-5650-4382-b958-b142a732fe74/final.cram, /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpi8cINA/stg219a0b23-e75f-4d26-94be-beec315b3fd7/final.cram] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpi8cINA/stgf8d0d17d-05e0-4a78-b9ee-77cb28cec072/94b23d66f667472690a7ee165e2037b6.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirvLWoCZ/docm_out.vcf likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[] excludeAnnotation=[] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=GENOTYPE_GIVEN_ALLELES alleles=(RodBinding name=alleles source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpi8cINA/stgab13654f-7c5a-4226-8df0-1ac602900441/snvs.hq.vcf.gz) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.LeftAlignAndTrimVariants=<ID=LeftAlignAndTrimVariants,Version=3.6-0-gf185a75,Date="Tue Sep 04 21:30:20 CDT 2018",Epoch=1536114620963,CommandLineOptions="analysis_type=LeftAlignAndTrimVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpPMoFQw/stga1868b1f-6dd8-49e8-9ad0-618a5c335c3f/merged.vcf.gz) dontTrimAlleles=false splitMultiallelics=true keepOriginalAC=false out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirmq70AZ/normalized.vcf.gz filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.MuTect2=<ID=MuTect2,Version=3.6-0-gf185a75,Date="Tue Sep 04 20:32:17 CDT 2018",Epoch=1536111137314,CommandLineOptions="analysis_type=MuTect2 input_file=[/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmphSAMcf/stgb2781d1e-daa3-4523-bf6f-95f13bce5408/final.cram, /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmphSAMcf/stg94e2fd6d-1c80-4941-b5f9-5e20be5213e4/final.cram] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmphSAMcf/stgf06c52f3-aa1a-4596-ba59-2bec4147be06/47.interval_list] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false m2debug=false artifact_detection_mode=true initial_tumor_lod=4.0 initial_normal_lod=0.5 tumor_lod=6.3 normal_lod=2.2 dbsnp_normal_lod=5.5 max_alt_alleles_in_normal_count=1 max_alt_alleles_in_normal_qscore_sum=20 max_alt_allele_in_normal_fraction=0.03 debug=false useFilteredReadsForAnnotations=false emitRefConfidence=NONE bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_num_PL_values=100 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=false kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 gcpHMM=10 pair_hmm_implementation=VECTOR_LOGLESS_CACHING pair_hmm_sub_implementation=ENABLE_ALL always_load_vector_logless_PairHMM_lib=false phredScaledGlobalReadMismappingRate=45 noFpga=false debug_read_name=null MQ_filtering_level=20 cosmic=[] normal_panel=[] dbsnp=(RodBinding name= source=UNBOUND) comp=[] annotation=[DepthPerAlleleBySample, BaseQualitySumPerAlleleBySample, TandemRepeatAnnotator, OxoGReadCounts] excludeAnnotation=[SpanningDeletions] out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirhz4NNn/mutect.vcf.gz dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 keepRG=null min_base_quality_score=10 errorCorrectReads=false captureAssemblyFailureBAM=false dontUseSoftClippedBases=false justDetermineActiveRegions=false doNotRunPhysicalPhasing=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.SelectVariants.2=<ID=SelectVariants,Version=3.6-0-gf185a75,Date="Tue Sep 04 21:13:57 CDT 2018",Epoch=1536113637270,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpnUregD/stg825ba0b4-8ec4-43e7-bf77-311b1066496b/strelka_full.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirWyLate/strelka_filtered.vcf.gz sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=true preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.6-0-gf185a75,Date="Tue Sep 04 21:50:17 CDT 2018",Epoch=1536115817853,CommandLineOptions="analysis_type=SelectVariants input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmp8YR0Ph/stg5061d161-bbfd-49aa-a124-cf7a540dc9e4/varscan_full.vcf.gz) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdir83BIdx/varscan_filtered.vcf.gz sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] exclude_sample_expressions=[] selectexpressions=[] invertselect=false excludeNonVariants=false excludeFiltered=true preserveAlleles=false removeUnusedAlternates=false restrictAllelesTo=ALL keepOriginalAC=false keepOriginalDP=false mendelianViolation=false invertMendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[] selectTypeToExclude=[] keepIDs=null excludeIDs=null fullyDecode=false justRead=false maxIndelSize=2147483647 minIndelSize=0 maxFilteredGenotypes=2147483647 minFilteredGenotypes=0 maxFractionFilteredGenotypes=1.0 minFractionFilteredGenotypes=0.0 maxNOCALLnumber=2147483647 maxNOCALLfraction=1.0 setFilteredGtToNocall=false ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES=false forceValidOutput=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##GATKCommandLine.VariantFiltration=<ID=VariantFiltration,Version=3.6-0-gf185a75,Date="Tue Sep 04 21:28:41 CDT 2018",Epoch=1536114521992,CommandLineOptions="analysis_type=VariantFiltration input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpuugz3F/stg98fe0847-0ac0-4d71-90f0-01f5365a87ba/output.snp.Somatic.vcf.gz) mask=(RodBinding name=mask source=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpuugz3F/stgbe957e74-8f78-481f-90e0-564b807e4954/output.snp.Somatic.hc.vcf.gz) out=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdir2Slmy2/output.vcf.gz filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=processSomatic filterNotInMask=true missingValuesInExpressionsShouldEvaluateAsFailing=false invalidatePreviousFilters=false invertFilterExpression=false invertGenotypeFilterExpression=false setFilteredGtToNocall=false filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=ECNT,Number=1,Type=String,Description="Number of events in this haplotype">
+##INFO=<ID=EQSI,Number=1,Type=Float,Description="Empirically calibrated quality score for somatic variants">
+##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=HCNT,Number=1,Type=String,Description="Number of haplotypes that support this variant">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=IC,Number=1,Type=Integer,Description="Number of times RU repeats in the indel allele">
+##INFO=<ID=IHP,Number=1,Type=Integer,Description="Largest reference interrupted homopolymer length intersecting with the indel">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MAX_ED,Number=1,Type=Integer,Description="Maximum distance between events in this active region">
+##INFO=<ID=MIN_ED,Number=1,Type=Integer,Description="Minimum distance between events in this active region">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MAPQ == 0 reads covering this record">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=NLOD,Number=1,Type=String,Description="Normal LOD score">
+##INFO=<ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##INFO=<ID=OVERLAP,Number=0,Type=Flag,Description="Somatic indel possibly overlaps a second indel.">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=PNOISE,Number=1,Type=Float,Description="Fraction of panel containing non-reference noise at this site">
+##INFO=<ID=PNOISE2,Number=1,Type=Float,Description="Fraction of panel containing more than one non-reference noise obs at this site">
+##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal">
+##INFO=<ID=QSI_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
+##INFO=<ID=QSS,Number=1,Type=Integer,Description="Quality score for any somatic snv, ie. for the ALT allele to be present at a significantly different frequency in the tumor and normal">
+##INFO=<ID=QSS_NT,Number=1,Type=Integer,Description="Quality score reflecting the joint probability of a somatic variant and NT">
+##INFO=<ID=RC,Number=1,Type=Integer,Description="Number of times RU repeats in the reference allele">
+##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
+##INFO=<ID=RU,Number=1,Type=String,Description="Smallest repeating sequence unit in inserted or deleted sequence">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref read-position in the tumor">
+##INFO=<ID=SGT,Number=1,Type=String,Description="Most likely somatic genotype excluding normal noise states">
+##INFO=<ID=SNVSB,Number=1,Type=Float,Description="Somatic SNV site strand bias">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SomaticEVS,Number=1,Type=Float,Description="Somatic Empirical Variant Score (EVS) expressing the phred-scaled probability of the call being a false positive observation.">
+##INFO=<ID=TLOD,Number=1,Type=String,Description="Tumor LOD score">
+##INFO=<ID=TQSI,Number=1,Type=Integer,Description="Data tier used to compute QSI">
+##INFO=<ID=TQSI_NT,Number=1,Type=Integer,Description="Data tier used to compute QSI_NT">
+##INFO=<ID=TQSS,Number=1,Type=Integer,Description="Data tier used to compute QSS">
+##INFO=<ID=TQSS_NT,Number=1,Type=Integer,Description="Data tier used to compute QSS_NT">
+##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
+##SAMPLE=<ID=NORMAL,SampleName=H_TC-GBM051-051-PBMCNorm-DNA,File=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmphSAMcf/stg94e2fd6d-1c80-4941-b5f9-5e20be5213e4/final.cram>
+##bcftools_annotateCommand=annotate -x INFO/END -Oz -o /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirZgTT_n/pindel.noend.vcf.gz /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpK2DsJv/stg2f951651-caf0-41e3-beb5-572922441572/select_variants.vcf.gz
+##bcftools_annotateVersion=1.3.1+htslib-1.3.1
+##bcftools_concatCommand=concat --allow-overlaps --remove-duplicates --output-type z -o /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdir7rykmX/merged.vcf.gz /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpXVpvBl/stgc94364f1-b286-455f-bd0f-12745c8827e5/output.vcf.gz /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpXVpvBl/stge869e321-3803-430b-9fa5-dd6f713b65b7/output.vcf.gz
+##bcftools_concatVersion=1.3.1+htslib-1.3.1
+##cmdline=/opt/strelka/bin/configureStrelkaSomaticWorkflow.py --runDir=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirzSHM4o --tumorBam=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmp2KoFyN/stgf21d4cf6-659b-4df5-93b4-8345a9f1256e/final.cram --normalBam=/gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmp2KoFyN/stge7391a87-f242-4191-a681-c4ed66ef4b85/final.cram --referenceFasta=/gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa --exome
+##content=strelka somatic snv calls
+##fileDate=20180904
+##priorSomaticIndelRate=1e-06
+##priorSomaticSnvRate=0.0001
+##reference=file:///gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa
+##source=SelectVariants
+##source_version=2.7.1
+##startTime=Tue Sep  4 20:37:14 2018
+##vcfProcessLog=<InputVCF=</gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpNqPfP_/stg639e5527-e26d-4d36-a94e-389f6d6e529e/normalized.vcf.gz>, InputVCFSource=<fpfilter>, InputVCFVer=<6.0>, InputVCFParam=<"--bam-readcount /usr/bin/bam-readcount --samtools /opt/samtools/bin/samtools --output /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/tmp/out_tmpdirzXtXlW/varscan_full.vcf --reference /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa --bam-file /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpNqPfP_/stg37224812-cdb6-409a-ae2d-642bd08b4b20/output.bam --vcf-file /gscmnt/gc2609/gbm_antigen_dunn/model_data/08771a105e164ea9b312c56807708ce4/builda7db4149ccb4428dbee639315379a959/results/tmpNqPfP_/stg639e5527-e26d-4d36-a94e-389f6d6e529e/normalized.vcf.gz --sample TUMOR --min-var-freq 0.1"> InputVCFgeneAnno=<.>>
+##VEP="v90" time="2018-09-04 23:51:32" cache="/gscmnt/gc2764/cad/ssiebert/toil_test/inputs/VEP_cache/homo_sapiens/90_GRCh38" ensembl-funcgen=90.743f32b ensembl=90.87ba57b ensembl-io=90.9a148ea ensembl-variation=90.00c29b7 1000genomes="phase3" COSMIC="81" ClinVar="201706" ESP="V2-SSA137" HGMD-PUBLIC="20164" assembly="GRCh38.p10" dbSNP="150" gencode="GENCODE 27" genebuild="2014-07" gnomAD="170228" polyphen="2.2.2" regbuild="16" sift="sift5.2.2"
+##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|PICK|SYMBOL_SOURCE|HGNC_ID|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
+##DownstreamProtein=Predicted downstream translation for frameshift mutations
+##ProteinLengthChange=Predicted change in protein product length
+##WildtypeProtein=The normal, non-mutated protein sequence
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand (high-quality bases)">
+##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
+chr1	1738993	.	T	C	.	PASS	AC=1;AF=0.25;AN=4;ECNT=1;HCNT=6;MAX_ED=.;MIN_ED=.;NLOD=19.93;TLOD=29.38;set=mutect;CSQ=C|synonymous_variant|LOW|SLC35E2|ENSG00000215790|Transcript|ENST00000246421|protein_coding|3/6||||803|387|129|L|ttA/ttG|||-1||1|HGNC|HGNC:20863||||||||||||||||||||||MSSSVKTPALEELVPGSEEKPKGRSPLSWGSLFGHRSEKIVFAKSDGGTDENVLTVTITETTVIESDLGVWSSRALLYLTLWFFFSFCTLFLNKYILSLLGGEPSMLGAVQMLSTTVIGCVKTLVPCCLYQHKARLSYPPNFLMTMLFVGLMRFATVVLGLVSLKNVAVSFAETVKSSAPIFTVIMSRMILGEYTGRPSDREEREELQLQPGRGAAASDRRSPVPPSERHGVRPHGENLPGDFQVPQALHRVALSMALPCPMLPAS,C|synonymous_variant|LOW|SLC35E2|ENSG00000215790|Transcript|ENST00000355439|protein_coding|4/7||||1148|387|129|L|ttA/ttG|||-1|||HGNC|HGNC:20863||||||||||||||||||||||MSSSVKTPALEELVPGSEEKPKGRSPLSWGSLFGHRSEKIVFAKSDGGTDENVLTVTITETTVIESDLGVWSSRALLYLTLWFFFSFCTLFLNKYILSLLGGEPSMLGAVQMLSTTVIGCVKTLVPCCLYQHKARLSYPPNFLMTMLFVGLMRFATVVLGLVSLKNVAVSFAETVKSSAPIFTVIMSRMILGEYTGRPSDREEREELQLQPGRGAAASDRRSPVPPSERHGVRPHGENLPGDFQAQ,C|downstream_gene_variant|MODIFIER|AL031282.1|ENSG00000227775|Transcript|ENST00000418950|transcribed_processed_pseudogene|||||||||||1742|1|||Clone_based_ensembl_gene|||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|AL031282.1|ENSG00000227775|Transcript|ENST00000424604|processed_transcript|||||||||||3018|1|||Clone_based_ensembl_gene|||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|SLC35E2|ENSG00000215790|Transcript|ENST00000475229|processed_transcript|||||||||||3373|-1|||HGNC|HGNC:20863||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|AL031282.1|ENSG00000227775|Transcript|ENST00000577672|processed_transcript|||||||||||3020|1|||Clone_based_ensembl_gene|||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|AL031282.2|ENSG00000268575|Transcript|ENST00000598846|processed_transcript|||||||||||1305|-1|||Clone_based_ensembl_gene|||||||||||||||||||||||	GT:AD:AF:DP:ADF:ADR	0/0:312,17:0.07:.:.:.	0/1:516,28:0.05128:546:251,24:265,4
diff --git a/tests/test_data/existing_sample.genotype.vcf b/tests/test_data/existing_sample.genotype.vcf
index 9cd1f10..e8e890a 100644
--- a/tests/test_data/existing_sample.genotype.vcf
+++ b/tests/test_data/existing_sample.genotype.vcf
@@ -79,4 +79,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
diff --git a/tests/test_data/hom_ref.readcount.vcf b/tests/test_data/hom_ref.readcount.vcf
index 79aef9a..2970129 100644
--- a/tests/test_data/hom_ref.readcount.vcf
+++ b/tests/test_data/hom_ref.readcount.vcf
@@ -150,4 +150,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
-chr22	36265781	.	T	G	.	PASS	AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC%3A618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC%3A618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP:ADF:ADR	0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212:108,0:99,5	0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383:.:.
+chr22	36265781	.	T	G	.	PASS	AC=1;AF=0.25;AN=4;ECNT=1;HCNT=18;MAX_ED=.;MIN_ED=.;NLOD=30.75;TLOD=16.26;set=mutect;CSQ=G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000319136|protein_coding|7/7||||1260|993|331|G|ggT/ggG|||1||1|HGNC|HGNC:618||||||||||||||||||||||MRFKSHTVELRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397278|protein_coding|6/6||||1174|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000397279|protein_coding|6/7||||1043|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000422471|nonsense_mediated_decay|||||||||||4108|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000422706|protein_coding|6/6||||1152|945|315|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|synonymous_variant|LOW|APOL1|ENSG00000100342|Transcript|ENST00000426053|protein_coding|5/5||||1059|891|297|G|ggT/ggG|||1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLRALADGVQKVHKGTTIANVVSGSLSISSGILTLVGMGLAPFTEGGSLVLLEPGMELGITAALTGITSSTMDYGKKWWTQAQAHDLVIKSLDKLKEVREFLGENISNFLSLAGNTYQLTRGIGKDIRALRRARANLQSVPHASASRPRVTEPISAESGEQVERVNEPSILEMSRGVKLTDVAPVSFFLVLDVVYLVYESKHLHEGAKSETAEELKKVAQELEEKLNILNNNYKILQADQEL,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000427990|protein_coding|||||||||||466|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLTDNEAWNGFVAAAELPRNEADELRKALDNLARQMIMKDKNWHDKGQQYRNWFLKEFPRLKSELEDNIRRLR,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000431184|nonsense_mediated_decay|||||||||||4148|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMVVVLNAVEFETLFLNFK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000433768|protein_coding|||||||||||4137|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000438034|protein_coding|||||||||||4106|1|cds_end_NF||HGNC|HGNC:618||||||||||||||||||||||MRFKSHTVELRSTLSQPLFSCSRRRPCSDMEGAALLRVSVLCIWMSALFLGVGVRAEEAGARVQQNVPSGTDTGDPQSKPLGDWAAGTMDPESSIFIEDAIKYFKEKVSTQNLLLLLT,G|downstream_gene_variant|MODIFIER|APOL1|ENSG00000100342|Transcript|ENST00000439680|nonsense_mediated_decay|||||||||||4082|1|||HGNC|HGNC:618||||||||||||||||||||||MEGAALLRVSVLCIWVQQNVPSGTDTGDPQSKPLGDWAAGTMDPGPAGSRGDSGEPCTLRPACRGQRQHGGASRISAEGPAPMPRRRTPSTAHLRVPKTSRRNLLCMRAVSLLRMPLSISRKK	GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1:DP:ADF:ADR	0/0:207,5:0.02358:0:4:0.0:4478,60:88:79:212:108,0:99,5	0/1:341,42:0.10966:1:61:0.016:8708,1130:190:119:383:.:.
diff --git a/tests/test_data/indel_mode.bam_readcount.vcf b/tests/test_data/indel_mode.bam_readcount.vcf
index c94f2a4..f0b87cd 100644
--- a/tests/test_data/indel_mode.bam_readcount.vcf
+++ b/tests/test_data/indel_mode.bam_readcount.vcf
@@ -84,7 +84,7 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-6	41754573	.	C	CCTT	.	.	CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1%3Ac.861_862insCTT|ENSP00000404911.1%3Ap.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF:ADF:ADR	0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421:13,26:9,26
-6	43250725	.	GGAA	G	.	.	CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4%3Ac.2248_2250delGAA|ENSP00000259750.4%3Ap.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF	0/1:0:43,47,54,56:34:2:0,0:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS:0
-22	16228619	.	T	C	.	.	CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC	1/1:0,5:42:2:7:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+6	41754573	.	C	CCTT	.	.	CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1:c.861_862insCTT|ENSP00000404911.1:p.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF:ADF:ADR	0/1:76:13,9,28,26:36:2:22,52:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS:0.68421:13,26:9,26
+6	43250725	.	GGAA	G	.	.	CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4:c.2248_2250delGAA|ENSP00000259750.4:p.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT:AF	0/1:0:43,47,54,56:34:2:0,0:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS:0
+22	16228619	.	T	C	.	.	CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1:n.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC	1/1:0,5:42:2:7:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
diff --git a/tests/test_data/info2_output.vcf b/tests/test_data/info2_output.vcf
index 44c0f4c..c4ddef5 100644
--- a/tests/test_data/info2_output.vcf
+++ b/tests/test_data/info2_output.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MAPQ == 0 reads covering this record">
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;MQ0=0	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+chr1	168192360	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;MQ0=0	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
diff --git a/tests/test_data/info3_output.vcf b/tests/test_data/info3_output.vcf
index 53ad544..0c58946 100644
--- a/tests/test_data/info3_output.vcf
+++ b/tests/test_data/info3_output.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##INFO=<ID=TEST,Number=1,Type=String,Description="test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;TEST=asdffdsa	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;TEST=asdffdsa	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
diff --git a/tests/test_data/info_annotation.vcf b/tests/test_data/info_annotation.vcf
index 89716c1..67fa95a 100644
--- a/tests/test_data/info_annotation.vcf
+++ b/tests/test_data/info_annotation.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="test">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;TEST=2	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC;TEST=2	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609
diff --git a/tests/test_data/input.cufflinks.gx.vcf b/tests/test_data/input.cufflinks.gx.vcf
index b5d0ec4..547faf7 100644
--- a/tests/test_data/input.cufflinks.gx.vcf
+++ b/tests/test_data/input.cufflinks.gx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|2.35912
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|2.35912
diff --git a/tests/test_data/input.cufflinks.tx.vcf b/tests/test_data/input.cufflinks.tx.vcf
index 61287fd..7de085f 100644
--- a/tests/test_data/input.cufflinks.tx.vcf
+++ b/tests/test_data/input.cufflinks.tx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=TX,Number=.,Type=String,Description="Transcript Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|2.35912
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|2.35912
diff --git a/tests/test_data/input.kallisto.gx.vcf b/tests/test_data/input.kallisto.gx.vcf
index a7873d0..890c5d3 100644
--- a/tests/test_data/input.kallisto.gx.vcf
+++ b/tests/test_data/input.kallisto.gx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|18.4008276190378
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|18.4008276190378
diff --git a/tests/test_data/input.kallisto.tx.vcf b/tests/test_data/input.kallisto.tx.vcf
index d16f1c4..188d90b 100644
--- a/tests/test_data/input.kallisto.tx.vcf
+++ b/tests/test_data/input.kallisto.tx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=TX,Number=.,Type=String,Description="Transcript Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|4
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|4
diff --git a/tests/test_data/input.kallisto.with_version.tx.vcf b/tests/test_data/input.kallisto.with_version.tx.vcf
index bd2fccf..53da72f 100644
--- a/tests/test_data/input.kallisto.with_version.tx.vcf
+++ b/tests/test_data/input.kallisto.with_version.tx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=TX,Number=.,Type=String,Description="Transcript Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794.1|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794.1|4
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794.1|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794.1|4
diff --git a/tests/test_data/input.stringtie.gx.vcf b/tests/test_data/input.stringtie.gx.vcf
index dda57f4..f6fffab 100644
--- a/tests/test_data/input.stringtie.gx.vcf
+++ b/tests/test_data/input.stringtie.gx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|2.629013
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENSG00000184979|2.629013
diff --git a/tests/test_data/input.stringtie.tx.vcf b/tests/test_data/input.stringtie.tx.vcf
index 097046c..bafd1a1 100644
--- a/tests/test_data/input.stringtie.tx.vcf
+++ b/tests/test_data/input.stringtie.tx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=TX,Number=.,Type=String,Description="Transcript Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|0.233563
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:TX	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:ENST00000215794|0.233563
diff --git a/tests/test_data/multiple_samples.gx.vcf b/tests/test_data/multiple_samples.gx.vcf
index 21b3060..9a282ac 100644
--- a/tests/test_data/multiple_samples.gx.vcf
+++ b/tests/test_data/multiple_samples.gx.vcf
@@ -80,4 +80,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395	H_NJ-HCC1395-HCC1396
-22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.
+22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1:n.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.
diff --git a/tests/test_data/multiple_samples.readcount.vcf b/tests/test_data/multiple_samples.readcount.vcf
index 3c3a076..d16ac69 100644
--- a/tests/test_data/multiple_samples.readcount.vcf
+++ b/tests/test_data/multiple_samples.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395	H_NJ-HCC1395-HCC1396
-22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.:.:.:.:.
+22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1:n.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:.:.:.:.:.
diff --git a/tests/test_data/multiple_samples_second_alt.readcount.vcf b/tests/test_data/multiple_samples_second_alt.readcount.vcf
index 3edb89c..f5419ed 100644
--- a/tests/test_data/multiple_samples_second_alt.readcount.vcf
+++ b/tests/test_data/multiple_samples_second_alt.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395	H_NJ-HCC1395-HCC1396
-22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.375,0.0:10,6,0:6,5,0:4,1,0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0
+22	16202096	.	C	A,T	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1:n.337-2143G>T||||	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:DP:AF:AD:ADF:ADR	0/1:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.375,0.0:10,6,0:6,5,0:4,1,0	0/2:.:2:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:16:0.37500,0.00000:10,6,0:6,5,0:4,1,0
diff --git a/tests/test_data/multiple_transcripts.gx.vcf b/tests/test_data/multiple_transcripts.gx.vcf
index e1d86cd..abad5b7 100644
--- a/tests/test_data/multiple_transcripts.gx.vcf
+++ b/tests/test_data/multiple_transcripts.gx.vcf
@@ -82,4 +82,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	16202096	.	C	A	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T||||,A|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:9,3:.:2:12:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0,ENSG00000235992|0.0229311
+22	16202096	.	C	A	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1:n.337-2143G>T||||,A|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1:n.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:9,3:.:2:12:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0,ENSG00000235992|0.0229311
diff --git a/tests/test_data/multiple_transcripts_one_missing_gene.gx.vcf b/tests/test_data/multiple_transcripts_one_missing_gene.gx.vcf
index e4bb29f..ec32204 100644
--- a/tests/test_data/multiple_transcripts_one_missing_gene.gx.vcf
+++ b/tests/test_data/multiple_transcripts_one_missing_gene.gx.vcf
@@ -82,4 +82,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GX,Number=.,Type=String,Description="Gene Expressions">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	16202096	.	C	A	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1%3An.337-2143G>T||||,A|MISSING_GENE|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:9,3:.:2:12:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0
+22	16202096	.	C	A	.	.	CSQ=A|ENSG00000225255|ENST00000453395|Transcript|intron_variant&nc_transcript_variant||||||||||||-1|YES|LA16c-83F12.6|Clone_based_vega_gene|||ENST00000453395.1:n.337-2143G>T||||,A|MISSING_GENE|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1:n.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:GQ:MQ:DP4:GX	0/1:9,3:.:2:12:0:0:0:4,4:12,12:2,2:0,0:PASS:0.25:11.1126:46:47:6,4,5,1:ENSG00000225255|0.0
diff --git a/tests/test_data/no_gt_in_format.genotype.vcf b/tests/test_data/no_gt_in_format.genotype.vcf
index ba88b5d..bddc4d9 100644
--- a/tests/test_data/no_gt_in_format.genotype.vcf
+++ b/tests/test_data/no_gt_in_format.genotype.vcf
@@ -79,4 +79,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395	TUMOR
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	.:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609	0/1:.:.:.:.:.:.:.:.:.:.:.:.
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	.:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609	0/1:.:.:.:.:.:.:.:.:.:.:.:.
diff --git a/tests/test_data/no_matching_readcount.readcount.vcf b/tests/test_data/no_matching_readcount.readcount.vcf
index bb12ed4..0d39f54 100644
--- a/tests/test_data/no_matching_readcount.readcount.vcf
+++ b/tests/test_data/no_matching_readcount.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644674	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0:0:0,0
+22	18644674	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0:0:0,0
diff --git a/tests/test_data/ref_transcript_mismatch_reporter/output.hard.filtered.vcf b/tests/test_data/ref_transcript_mismatch_reporter/output.hard.filtered.vcf
old mode 100755
new mode 100644
diff --git a/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf b/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf
index 1e3106c..87303d2 100644
--- a/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf
+++ b/tests/test_data/ref_transcript_mismatch_reporter/output.no_protein_pos.filtered.vcf
@@ -266,4 +266,4 @@
 ##FrameshiftSequence=Predicted sequence for frameshift mutations
 ##WildtypeProtein=The normal, non-mutated protein sequence
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CV023_N	CV023_T
-chr19	45408613	.	G	GA,GAA	.	multiallelic;normal_artifact;slippage	AS_FilterStatus=SITE|weak_evidence,strand_bias;AS_SB_TABLE=145%2C61|15%2C2|4%2C0;DP=240;ECNT=1;GERMQ=93;MBQ=34,34,34;MFRL=275,273,342;MMQ=60,60,60;MPOS=44,7;NALOD=-1.648,1.19;NLOD=7.08,12.31;POPAF=4.31,6.0;RPA=8,9,10;RU=A;STR;STRQ=1;TLOD=15.84,4.67;CSQ=A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8%3Ac.*1061dup||2099-2100|||||||-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8%3Ac.*1060_*1061dup||2099-2100|||||||-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8%3Ac.653dup|ENSP00000310966.3%3Ap.Asn218LysfsTer58|698-699|645-646|215-216|-/X|-/A|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8%3Ac.652_653dup|ENSP00000310966.3%3Ap.Asn218LysfsTer5|698-699|653-654|218|N/X|-/AA|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC%3A3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC%3A18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6%3Ac.*1061dup||1839-1840|||||||-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6%3Ac.*1060_*1061dup||1839-1840|||||||-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC%3A18838|2|||,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC%3A18838|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC%3A3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC%3A3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC%3A3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC%3A3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1%3Ac.659dup|ENSP00000465099.1%3Ap.Asn220LysfsTer58|657-658|651-652|217-218|-/X|-/A|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1%3Ac.658_659dup|ENSP00000465099.1%3Ap.Asn220LysfsTer5|657-658|659-660|220|N/X|-/AA|||1||HGNC|HGNC%3A24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC%3A3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC%3A3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,A|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC%3A24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,AA|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC%3A24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC%3A3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC%3A3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC%3A3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC%3A3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC%3A3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112|37-38|-/X|-/A|||1|cds_end_NF|HGNC|HGNC%3A24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112||-/X|-/AA|||1|cds_end_NF|HGNC|HGNC%3A24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC%3A18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:49,2,0:0.065,0.022:51:28,1,0:6,1,0:41,2,0:30,19,2,0	0/1/2:157,15,4:0.083,0.03:176:18,2,0:111,11,4:146,13,4:115,42,17,2
+chr19	45408613	.	G	GA,GAA	.	multiallelic;normal_artifact;slippage	AS_FilterStatus=SITE|weak_evidence,strand_bias;AS_SB_TABLE=145%2C61|15%2C2|4%2C0;DP=240;ECNT=1;GERMQ=93;MBQ=34,34,34;MFRL=275,273,342;MMQ=60,60,60;MPOS=44,7;NALOD=-1.648,1.19;NLOD=7.08,12.31;POPAF=4.31,6.0;RPA=8,9,10;RU=A;STR;STRQ=1;TLOD=15.84,4.67;CSQ=A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000013807|protein_coding|||||||||||4820|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8:c.*1061dup||2099-2100|||||||-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000300853|protein_coding|10/10||ENST00000300853.8:c.*1060_*1061dup||2099-2100|||||||-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8:c.653dup|ENSP00000310966.3:p.Asn218LysfsTer58|698-699|645-646|215-216|-/X|-/A|||1||HGNC|HGNC:24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000309424|protein_coding|3/3||ENST00000309424.8:c.652_653dup|ENSP00000310966.3:p.Asn218LysfsTer5|698-699|653-654|218|N/X|-/AA|||1||HGNC|HGNC:24219|1|8|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000340192|protein_coding|||||||||||1000|-1||HGNC|HGNC:3433|1|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000360957|protein_coding|||||||||||3544|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000418234|protein_coding|||||||||||2264|-1||HGNC|HGNC:18838|1|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQPDAYGSLDRATSPRPRAFDGAGSSLGRAPSPRPGPGPLRQQGPPTPFDFLGRAGSPRGSPLAEGPQAFFPERGPSPRPPATAYDAPASAFGSSLLGSGGSAFAPPLRAQDDLTLRRRPPKAWNESDLDVAYEKKPSQTASYERLDVFARPASPSLQLLPWRESSLDGLGGTGKDNLTSATLPRNYKVSPLASDRRSDAGSYRRSLGSAGPSGTLPRSWQPVSRIPMPPSSPQPRGAPRQRPIPLSMIFKLQNAFWEHGASRAMLPGSPLFTRAPPPKLQPQPQPQPQPQSQPQPQLPPQPQTQPQTPTPAPQHPQQTWPPVNEGPPKPPTELEPEPEIEGLLTPVLEAGDVDEGPVARPLSPTRLQPALPPEAQSVPELEEVARVLAEIPRPLKRRGSMEQAPAVALPPTHKKQYQQIISRLFHRHGGPGPGGPEPELSPITEGSEARAGPPAPAPPAPIPPPAPSQSSPPEQPQSMEMRSVLRKAGSPRKARRARLNPLVLLLDAALTGELEVVQQAVKEMNDPSQPNEEGITALHNAICGANYSIVDFLITAGANVNSPDSHGWTPLHCAASCNDTVICMALVQHGAAIFATTLSDGATAFEKCDPYREGYADCATYLADVEQSMGLMNSGAVYALWDYSAEFGDELSFREGESVTVLRRDGPEETDWWWAALHGQEGYVPRNYFGLFPRVKPQRSKV,A|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6:c.*1061dup||1839-1840|||||||-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|3_prime_UTR_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000423698|protein_coding|9/9||ENST00000423698.6:c.*1060_*1061dup||1839-1840|||||||-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC:18838|2|||,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000585905|retained_intron|||||||||||2304|-1||HGNC|HGNC:18838|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC:3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000588738|processed_transcript|||||||||||932|-1||HGNC|HGNC:3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC:3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000589165|protein_coding|||||||||||1054|-1||HGNC|HGNC:3433|5|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQKARRLFDVLHEPFLKVP,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1:c.659dup|ENSP00000465099.1:p.Asn220LysfsTer58|657-658|651-652|217-218|-/X|-/A|||1||HGNC|HGNC:24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKSAAERTRGSRACGDRAHSGDTGASGSAVPVHHQEEEEAQRERNLRARRQDSEAGTD|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000589804|protein_coding|3/3||ENST00000589804.1:c.658_659dup|ENSP00000465099.1:p.Asn220LysfsTer5|657-658|659-660|220|N/X|-/AA|||1||HGNC|HGNC:24219|1|8|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKKISS|MEEPQAGGEDAARFSCPPNFTAKPPASESPRFSLEALTGPDTELWLIQAPADFAPECFNGRHVPLSGSQIVKGKLAGKRHRYRVLSSCPQAGEATLLAPSTEAGGGLTCASAPQGTLRILEGPQQSLSGSPLQPIPASPPPQIPPGLRPRFCAFGGNPPVTGPRSALAPNLLTSGKKKKEMQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKKNQQLKEPEAAGPVGTEPTVETLEPLGVLFPSTTKKRKKPKGKETFEPEDKTVKQEQINTEPLEDTVLSPTKKRKRQKGTEGMEPEEGVTVESQPQVKVEPLEEAIPLPPTKKRKKEKGQMAMMEPGTEAMEPVEPEMKPLESPGGTMAPQQPEGAKPQAQAALAAPKKKTKKEKQQDATVEPETEVVGPELPDDLEPQAAPTSTKKKKKKKERGHTVTEPIQPLEPELPGEGQPEARATPGSTKKRKKQSQESRMPETVPQEEMPGPPLNSESGEEAPTGRDKKRKQQQQQPV,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC:3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000590701|protein_coding|||||||||||1002|-1|cds_start_NF|HGNC|HGNC:3433|3|||XNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWSLWNSSSPHQEKIWPYAQAWALRKPGGCLMSCTSPS,A|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC:24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,AA|downstream_gene_variant|MODIFIER|POLR1G|ENSG00000117877|Transcript|ENST00000590794|protein_coding|||||||||||12|1|cds_start_NF|HGNC|HGNC:24219|5|||XEEPQAGASMGGMCLSLAPRSSRANWQASGTAIESSAAVPKLEKRPCWPPQRRQEVDSPVPQPPRAP,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000591636|protein_coding|||||||||||1005|-1||HGNC|HGNC:3433|2|||MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVAKPLFRSTQSLPTVDTSAQAAPQTYAEYAISQPLEGAGATCPTGSEPLAGETPNQALKPGAKSNSIIVSPRQRGNPVLKFVRNVPWEFGDVIPDYVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKELAKMCILADCTLILAWRPGGCLMSCTSPS,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000592134|protein_coding|||||||||||3550|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQ,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC:3433|2|||,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592410|processed_transcript|||||||||||4822|-1||HGNC|HGNC:3433|2|||,A|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC:3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,AA|downstream_gene_variant|MODIFIER|ERCC1|ENSG00000012061|Transcript|ENST00000592444|protein_coding|||||||||||4822|-1|cds_start_NF|HGNC|HGNC:3433|2|||XCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRSLEQLIAASREDLALCPGLGPQKVRALGKNPRSWGKERAPNKHNLRPQSFKVKKEPKTRHSGFRL,A|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112|37-38|-/X|-/A|||1|cds_end_NF|HGNC|HGNC:24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,AA|frameshift_variant|HIGH|POLR1G|ENSG00000117877|Transcript|ENST00000592852|protein_coding|2/2||||1055-1056|111-112||-/X|-/AA|||1|cds_end_NF|HGNC|HGNC:24219|2||MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK|MQVTEAPVTQEAVNGHGALEVDMALGSPEMDVRKKKKKK,A|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ,AA|upstream_gene_variant|MODIFIER|PPP1R13L|ENSG00000104881|Transcript|ENST00000593226|protein_coding|||||||||||2286|-1|cds_end_NF|HGNC|HGNC:18838|3|||MDSEAFQSARDFLDMNFQSLAMKHMDLKQMELDTAAAKVDELTKQLESLWSDSPAPPGPQAGPPSRPPRYSSSSIPEPFGSRGSPRKAATDGADTPFGRSESAPTLHPYSPLSPKGRPSSPRTPLYLQ	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/0:49,2,0:0.065,0.022:51:28,1,0:6,1,0:41,2,0:30,19,2,0	0/1/2:157,15,4:0.083,0.03:176:18,2,0:111,11,4:146,13,4:115,42,17,2
diff --git a/tests/test_data/single_sample.dna.readcount.vcf b/tests/test_data/single_sample.dna.readcount.vcf
index 2042a27..5defeed 100644
--- a/tests/test_data/single_sample.dna.readcount.vcf
+++ b/tests/test_data/single_sample.dna.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD:ADF:ADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD:ADF:ADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
diff --git a/tests/test_data/single_sample.genotype.vcf b/tests/test_data/single_sample.genotype.vcf
index 653d1d3..3b2a5e6 100644
--- a/tests/test_data/single_sample.genotype.vcf
+++ b/tests/test_data/single_sample.genotype.vcf
@@ -79,4 +79,4 @@
 ##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Allele|Gene|Feature|Feature_type|Consequence|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|DISTANCE|STRAND|CANONICAL|SYMBOL|SYMBOL_SOURCE|SIFT|PolyPhen|HGVSc|HGVSp|DownstreamProtein|ProteinLengthChange|WildtypeProtein">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395	TUMOR
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609	0/1:.:.:.:.:.:.:.:.:.:.:.:.
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609	0/1:.:.:.:.:.:.:.:.:.:.:.:.
diff --git a/tests/test_data/single_sample.rna.readcount.vcf b/tests/test_data/single_sample.rna.readcount.vcf
index 8a79107..75ef3ef 100644
--- a/tests/test_data/single_sample.rna.readcount.vcf
+++ b/tests/test_data/single_sample.rna.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=RADR,Number=R,Type=Integer,Description="RNA Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=RAF,Number=A,Type=Float,Description="RNA Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:RDP:RAF:RAD:RADF:RADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:RDP:RAF:RAD:RADF:RADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
diff --git a/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf b/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf
index 5bd98fa..8fa7700 100644
--- a/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf
+++ b/tests/test_data/single_sample_with_existing_readcount_annotations.readcount.vcf
@@ -84,4 +84,4 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:AF:ADF:ADR	0/1:102,5:.:2:107:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0.04673:43,3:59,2
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:AF:ADF:ADR	0/1:102,5:.:2:107:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:0.04673:43,3:59,2
diff --git a/tests/test_data/snv_mode.bam_readcount.vcf b/tests/test_data/snv_mode.bam_readcount.vcf
index f863672..d872f71 100644
--- a/tests/test_data/snv_mode.bam_readcount.vcf
+++ b/tests/test_data/snv_mode.bam_readcount.vcf
@@ -84,7 +84,7 @@
 ##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand (high-quality bases)">
 ##FORMAT=<ID=AF,Number=A,Type=Float,Description="Variant-allele frequency for the alt alleles">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
-6	41754573	.	C	CCTT	.	.	CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1%3Ac.861_862insCTT|ENSP00000404911.1%3Ap.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:76:13,9,28,26:36:2:12:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS
-6	43250725	.	GGAA	G	.	.	CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4%3Ac.2248_2250delGAA|ENSP00000259750.4%3Ap.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:200:43,47,54,56:34:2:56:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS
-22	16228619	.	T	C	.	.	CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1%3An.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC:AF	1/1:0,0:42:2:0:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60:0
-22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7%3Ac.371C>T|ENSP00000215794.7%3Ap.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD:ADF:ADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
+6	41754573	.	C	CCTT	.	.	CSQ=CTT|ENSG00000124593|ENST00000458694|Transcript|inframe_insertion|1109-1110|861-862|287-288|-/L|-/CTT|||||||1|YES|PRICKLE4|HGNC|||ENST00000458694.1:c.861_862insCTT|ENSP00000404911.1:p.Leu287dup|||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:76:13,9,28,26:36:2:12:78:12,12:55,55:12,12:80.52:1.92:0.0:PASS
+6	43250725	.	GGAA	G	.	.	CSQ=-|ENSG00000146216|ENST00000259750|Transcript|inframe_deletion|2331-2333|2248-2250|750|E/-|GAA/-|||||||1|YES|TTBK1|HGNC|||ENST00000259750.4:c.2248_2250delGAA|ENSP00000259750.4:p.Glu750del|||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:200:43,47,54,56:34:2:56:215:56,57:123,123:37,37:205.2:7.66:0.0:PASS
+22	16228619	.	T	C	.	.	CSQ=C|ENSG00000235992|ENST00000423297|Transcript|non_coding_exon_variant&nc_transcript_variant|909|||||||||||1|YES|GRAMD4P2|HGNC|||ENST00000423297.1:n.909T>C||||	GT:AD:BQ:SS:DP:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:IGT:DP4:BCOUNT:GQ:JGQ:VAQ:MQ:AMQ:SSC:AF	1/1:0,0:42:2:0:0:0:0:0,0:5,5:0,0:0,0:PASS:1.0:14.0313:1/1:0,0,3,4:0,5,0,0:39:.:42:49:57:60:0
+22	18644673	.	C	T	.	.	CSQ=T|ENSG00000184979|ENST00000215794|Transcript|missense_variant|801|371|124|A/V|gCc/gTc|||||||1|YES|USP18|HGNC|tolerated(1)|benign(0.162)|ENST00000215794.7:c.371C>T|ENSP00000215794.7:p.Ala124Val|||MSKAFGLLRQICQSILAESSQSPADLEEKKEEDSNMKREQPRERPRAWDYPHGLVGLHNIGQTCCLNSLIQVFVMNVDFTRILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVRPLELAYCLQKCNVPLFVQHDAAQLYLKLWNLIKDQITDVHLVERLQALYTIRVKDSLICVDCAMESSRNSSMLTLPLSLFDVDSKPLKTLEDALHCFFQPRELSSKSKCFCENCGKKTRGKQVLKLTHLPQTLTIHLMRFSIRNSQTRKICHSLYFPQSLDFSQILPMKRESCDAEEQSGGQYELFAVIAHVGMADSGHYCVYIRNAVDGKWFCFNDSNICLVSWEDIQCTYGNPNYHWQETAYLLVYMKMEC	GT:BQ:SS:FDP:SDP:SUBDP:AU:CU:GU:TU:FT:FA:TLOD:DP:AF:AD:ADF:ADR	0/1:.:2:1:0:0:0,0:106,108:0,0:6,6:PASS:0.04:7.56609:107:0.04673:102,5:43,3:59,2
diff --git a/tests/test_ref_transcript_mismatch_reporter.py b/tests/test_ref_transcript_mismatch_reporter.py
index d5c0917..3912e5a 100644
--- a/tests/test_ref_transcript_mismatch_reporter.py
+++ b/tests/test_ref_transcript_mismatch_reporter.py
@@ -10,6 +10,8 @@
 from testfixtures import LogCapture, StringComparison as S
 from io import StringIO
 from unittest.mock import patch
+import shutil
+from distutils.util import strtobool
 
 class RefTranscriptMismatchReporterTests(unittest.TestCase):
     @classmethod
@@ -17,6 +19,7 @@ def setUpClass(cls):
         base_dir          = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
         cls.executable    = os.path.join(base_dir, 'vatools', 'ref_transcript_mismatch_reporter.py')
         cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data', 'ref_transcript_mismatch_reporter')
+        cls.REGENERATE_TEST_DATA = strtobool(os.environ.get('REGENERATE_TEST_DATA', 'false'))
 
     def test_source_compiles(self):
         self.assertTrue(py_compile.compile(self.executable))
@@ -40,6 +43,11 @@ def test_no_filter(self):
                 os.path.join(temp_path.name, 'input.vcf'),
             ]
             ref_transcript_mismatch_reporter.main(command)
+            if self.REGENERATE_TEST_DATA:
+                shutil.copy(
+                    os.path.join(temp_path.name, 'input.mismatches.tsv'),
+                    os.path.join(self.test_data_dir, 'output.mismatches.tsv'),
+                )
             self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.mismatches.tsv'), os.path.join(temp_path.name, 'input.mismatches.tsv')))
             temp_path.cleanup()
             self.assertTrue("Total number of variants: 2" in str(l))
@@ -54,6 +62,11 @@ def test_soft_filter(self):
             "soft"
         ]
         ref_transcript_mismatch_reporter.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.filtered.vcf'),
+                os.path.join(self.test_data_dir, 'output.soft.filtered.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.soft.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
 
@@ -66,6 +79,11 @@ def test_hard_filter(self):
             "hard"
         ]
         ref_transcript_mismatch_reporter.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.filtered.vcf'),
+                os.path.join(self.test_data_dir, 'output.hard.filtered.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.hard.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
 
@@ -78,6 +96,11 @@ def test_no_protein_position_filter(self):
             "hard"
         ]
         ref_transcript_mismatch_reporter.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.filtered.vcf'),
+                os.path.join(self.test_data_dir, 'output.no_protein_pos.filtered.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.no_protein_pos.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
 
@@ -90,5 +113,10 @@ def test_protein_coding(self):
             "hard"
         ]
         ref_transcript_mismatch_reporter.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.filtered.vcf'),
+                os.path.join(self.test_data_dir, 'output.protein_coding.filtered.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'output.protein_coding.filtered.vcf'), os.path.join(temp_path.name, 'input.filtered.vcf')))
         temp_path.cleanup()
diff --git a/tests/test_vcf_expression_annotator.py b/tests/test_vcf_expression_annotator.py
index 276ba10..c53ea1f 100644
--- a/tests/test_vcf_expression_annotator.py
+++ b/tests/test_vcf_expression_annotator.py
@@ -7,13 +7,16 @@
 from filecmp import cmp
 import logging
 from testfixtures import LogCapture, StringComparison as S
+import shutil
+from distutils.util import strtobool
 
-class VcfExpressionEncoderTests(unittest.TestCase):
+class VcfExpressionAnnotatorTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         base_dir          = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
         cls.executable    = os.path.join(base_dir, 'vatools', 'vcf_expression_annotator.py')
         cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data')
+        cls.REGENERATE_TEST_DATA = strtobool(os.environ.get('REGENERATE_TEST_DATA', 'false'))
 
     def test_source_compiles(self):
         self.assertTrue(py_compile.compile(self.executable))
@@ -149,6 +152,11 @@ def test_skip_variant_without_gene_in_csq(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'input.ensr_transcript.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.ensr_transcript.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -178,6 +186,11 @@ def test_multi_sample_vcf(self):
             '-s', 'H_NJ-HCC1395-HCC1395',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'multiple_samples.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_samples.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -191,6 +204,11 @@ def test_multiple_transcripts(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'multiple_transcripts.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_transcripts.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -204,6 +222,11 @@ def test_multiple_transcripts_with_one_missing_gene(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'multiple_transcripts_one_missing_gene.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_transcripts_one_missing_gene.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -217,6 +240,11 @@ def test_cufflinks_format_gene_mode(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'input.cufflinks.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.cufflinks.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -230,6 +258,11 @@ def test_cufflinks_format_transcript_mode(self):
             'transcript',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.cufflinks.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.cufflinks.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
 
@@ -243,6 +276,11 @@ def test_kallisto_format_gene_mode(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'input.kallisto.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -256,6 +294,11 @@ def test_kallisto_format_transcript_mode(self):
             'transcript',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.kallisto.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
 
@@ -269,6 +312,11 @@ def test_stringtie_format_gene_mode(self):
             'gene',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.gx.vcf'),
+                os.path.join(self.test_data_dir, 'input.stringtie.gx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.stringtie.gx.vcf'), os.path.join(temp_path.name, 'input.gx.vcf')))
         temp_path.cleanup()
 
@@ -282,6 +330,11 @@ def test_stringtie_format_transcript_mode(self):
             'transcript',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.stringtie.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.stringtie.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
 
@@ -296,6 +349,11 @@ def test_kallisto_with_transcript_version_in_vcf(self):
             "--ignore-ensembl-id-version",
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.kallisto.with_version.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.with_version.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
 
@@ -310,6 +368,11 @@ def test_kallisto_with_transcript_version_in_expression_file(self):
             "--ignore-ensembl-id-version",
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.kallisto.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.kallisto.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
 
@@ -353,5 +416,10 @@ def test_skip_ENSR_transcript(self):
             'transcript',
         ]
         vcf_expression_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.tx.vcf'),
+                os.path.join(self.test_data_dir, 'input.ensr_transcript.tx.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'input.ensr_transcript.tx.vcf'), os.path.join(temp_path.name, 'input.tx.vcf')))
         temp_path.cleanup()
diff --git a/tests/test_vcf_genotype_annotator.py b/tests/test_vcf_genotype_annotator.py
index 28a1322..c029ba9 100644
--- a/tests/test_vcf_genotype_annotator.py
+++ b/tests/test_vcf_genotype_annotator.py
@@ -5,13 +5,16 @@
 from vatools import vcf_genotype_annotator
 import tempfile
 from filecmp import cmp
+import shutil
+from distutils.util import strtobool
 
-class VcfExpressionEncoderTests(unittest.TestCase):
+class VcfGenotypeAnnotatorTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         base_dir          = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
         cls.executable    = os.path.join(base_dir, 'vatools', 'vcf_genotype_annotator.py')
         cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data')
+        cls.REGENERATE_TEST_DATA = strtobool(os.environ.get('REGENERATE_TEST_DATA', 'false'))
 
     def test_source_compiles(self):
         self.assertTrue(py_compile.compile(self.executable))
@@ -35,6 +38,11 @@ def test_no_sample_vcf(self):
             '0/1',
         ]
         vcf_genotype_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.genotype.vcf'),
+                os.path.join(self.test_data_dir, 'no_sample.genotype.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'no_sample.genotype.vcf'), os.path.join(temp_path.name, 'input.genotype.vcf')))
         temp_path.cleanup()
 
@@ -47,6 +55,11 @@ def test_single_sample_vcf(self):
             '0/1',
         ]
         vcf_genotype_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.genotype.vcf'),
+                os.path.join(self.test_data_dir, 'single_sample.genotype.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'single_sample.genotype.vcf'), os.path.join(temp_path.name, 'input.genotype.vcf')))
         temp_path.cleanup()
 
@@ -59,6 +72,11 @@ def test_no_gt_in_format(self):
             '0/1',
         ]
         vcf_genotype_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.genotype.vcf'),
+                os.path.join(self.test_data_dir, 'no_gt_in_format.genotype.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'no_gt_in_format.genotype.vcf'), os.path.join(temp_path.name, 'input.genotype.vcf')))
         temp_path.cleanup()
 
@@ -71,5 +89,10 @@ def test_adding_gt_in_existing_sample(self):
             '0/1',
         ]
         vcf_genotype_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.genotype.vcf'),
+                os.path.join(self.test_data_dir, 'existing_sample.genotype.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'existing_sample.genotype.vcf'), os.path.join(temp_path.name, 'input.genotype.vcf')))
         temp_path.cleanup()
diff --git a/tests/test_vcf_info_annotator.py b/tests/test_vcf_info_annotator.py
index 7a0ee0d..675c481 100644
--- a/tests/test_vcf_info_annotator.py
+++ b/tests/test_vcf_info_annotator.py
@@ -5,13 +5,16 @@
 from vatools import vcf_info_annotator
 import tempfile
 from filecmp import cmp
+import shutil
+from distutils.util import strtobool
 
-class VcfInfoEncoderTests(unittest.TestCase):
+class VcfInfoAnnotatorTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         base_dir          = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
         cls.executable    = os.path.join(base_dir, 'vatools', 'vcf_info_annotator.py')
         cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data')
+        cls.REGENERATE_TEST_DATA = strtobool(os.environ.get('REGENERATE_TEST_DATA', 'false'))
 
     def test_source_compiles(self):
         self.assertTrue(py_compile.compile(self.executable))
@@ -65,6 +68,11 @@ def test_simple_caseq(self):
             '-o', os.path.join(temp_path.name, 'info_annotation.vcf')
         ]
         vcf_info_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'info_annotation.vcf'),
+                os.path.join(self.test_data_dir, 'info_annotation.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info_annotation.vcf'), os.path.join(temp_path.name, 'info_annotation.vcf')))
         temp_path.cleanup()
 
@@ -80,6 +88,11 @@ def test_simple_string(self):
             '-o', os.path.join(temp_path.name, 'info3_output.vcf')
         ]
         vcf_info_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'info3_output.vcf'),
+                os.path.join(self.test_data_dir, 'info3_output.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info3_output.vcf'), os.path.join(temp_path.name, 'info3_output.vcf')))
         temp_path.cleanup()
 
@@ -94,6 +107,11 @@ def test_addwhile_overwriteset(self):
             '-o', os.path.join(temp_path.name, 'info2_output.vcf')
         ]
         vcf_info_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'info2_output.vcf'),
+                os.path.join(self.test_data_dir, 'info2_output.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info2_output.vcf'), os.path.join(temp_path.name, 'info2_output.vcf')))
         temp_path.cleanup()
 
@@ -110,5 +128,10 @@ def test_overwrite_existing_field(self):
             '-o', os.path.join(temp_path.name, 'info_annotation.vcf')
         ]
         vcf_info_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'info_annotation.vcf'),
+                os.path.join(self.test_data_dir, 'info_overwrite.vcf'),
+            )
         self.assertTrue(cmp(os.path.join(self.test_data_dir, 'info_overwrite.vcf'), os.path.join(temp_path.name, 'info_annotation.vcf')))
         temp_path.cleanup()
diff --git a/tests/test_vcf_readcount_annotator.py b/tests/test_vcf_readcount_annotator.py
index cfa4bd3..0ed5cb9 100644
--- a/tests/test_vcf_readcount_annotator.py
+++ b/tests/test_vcf_readcount_annotator.py
@@ -8,13 +8,16 @@
 import io
 import logging
 from testfixtures import LogCapture, StringComparison as S
+import shutil
+from distutils.util import strtobool
 
-class VcfExpressionEncoderTests(unittest.TestCase):
+class VcfReadcountAnnotatorTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         base_dir          = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
         cls.executable    = os.path.join(base_dir, 'vatools', 'vcf_readcount_annotator.py')
         cls.test_data_dir = os.path.join(base_dir, 'tests', 'test_data')
+        cls.REGENERATE_TEST_DATA = strtobool(os.environ.get('REGENERATE_TEST_DATA', 'false'))
 
     def test_source_compiles(self):
         self.assertTrue(py_compile.compile(self.executable))
@@ -49,7 +52,15 @@ def test_single_sample_vcf_without_readcounts_annotations_dna_mode(self):
             'DNA',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'single_sample.dna.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'single_sample.dna.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'single_sample.dna.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_single_sample_vcf_without_readcounts_annotations_rna_mode(self):
@@ -61,7 +72,15 @@ def test_single_sample_vcf_without_readcounts_annotations_rna_mode(self):
             'RNA',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'single_sample.rna.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'single_sample.rna.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'single_sample.rna.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_single_sample_vcf_with_existing_readcount_annotations(self):
@@ -73,7 +92,15 @@ def test_single_sample_vcf_with_existing_readcount_annotations(self):
             'DNA',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'single_sample_with_existing_readcount_annotations.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'single_sample_with_existing_readcount_annotations.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'single_sample_with_existing_readcount_annotations.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_mutation_without_matching_readcount_value(self):
@@ -85,7 +112,15 @@ def test_mutation_without_matching_readcount_value(self):
             'DNA',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'no_matching_readcount.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'no_matching_readcount.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'no_matching_readcount.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_multi_sample_vcf(self):
@@ -98,7 +133,15 @@ def test_multi_sample_vcf(self):
             '-s', 'H_NJ-HCC1395-HCC1395',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_samples.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'multiple_samples.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'multiple_samples.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_multiple_alts(self):
@@ -111,7 +154,15 @@ def test_multiple_alts(self):
             '-s', 'H_NJ-HCC1395-HCC1396',
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'multiple_samples_second_alt.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'multiple_samples_second_alt.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'multiple_samples_second_alt.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_input_AF_is_of_number_1(self):
@@ -124,6 +175,16 @@ def test_input_AF_is_of_number_1(self):
             '-s', 'TUMOR'
         ]
         vcf_readcount_annotator.main(command)
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'af_number_1.bam-readcount.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'af_number_1.bam-readcount.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
+        temp_path.cleanup()
 
     def test_hom_ref_genotype(self):
         temp_path = tempfile.TemporaryDirectory()
@@ -135,7 +196,15 @@ def test_hom_ref_genotype(self):
             '-s', 'NORMAL'
         ]
         vcf_readcount_annotator.main(command)
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'hom_ref.readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'hom_ref.readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'hom_ref.readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_duplicate_bam_readcount_entries_discrepant_depth(self):
@@ -155,7 +224,15 @@ def test_duplicate_bam_readcount_entries_discrepant_depth(self):
             #a list of tuples. grab the relevant (and in this case only) tuple, the first, then combine into one string for comparison
             self.assertTrue(warn_message in logged_str)
 
-            self.assertTrue(cmp(os.path.join(self.test_data_dir, 'duplicate_entries_discrepant_depths.bam_readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+            if self.REGENERATE_TEST_DATA:
+                shutil.copy(
+                    os.path.join(temp_path.name, 'input.readcount.vcf'),
+                    os.path.join(self.test_data_dir, 'duplicate_entries_discrepant_depths.bam_readcount.vcf'),
+                )
+            self.assertTrue(cmp(
+                os.path.join(self.test_data_dir, 'duplicate_entries_discrepant_depths.bam_readcount.vcf'),
+                os.path.join(temp_path.name, 'input.readcount.vcf')
+            ))
         temp_path.cleanup()
 
     def test_duplicate_bam_readcount_entries_same_depth(self):
@@ -173,7 +250,15 @@ def test_duplicate_bam_readcount_entries_same_depth(self):
             logged_str = "".join(l.actual()[0])
             self.assertTrue(warn_message in logged_str)
 
-            self.assertTrue(cmp(os.path.join(self.test_data_dir, 'duplicate_entries_same_depths.bam_readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+            if self.REGENERATE_TEST_DATA:
+                shutil.copy(
+                    os.path.join(temp_path.name, 'input.readcount.vcf'),
+                    os.path.join(self.test_data_dir, 'duplicate_entries_same_depths.bam_readcount.vcf'),
+                )
+            self.assertTrue(cmp(
+                os.path.join(self.test_data_dir, 'duplicate_entries_same_depths.bam_readcount.vcf'),
+                os.path.join(temp_path.name, 'input.readcount.vcf')
+            ))
         temp_path.cleanup()
 
     def test_snv_mode(self):
@@ -187,7 +272,15 @@ def test_snv_mode(self):
         ]
         vcf_readcount_annotator.main(command)
 
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'snv_mode.bam_readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'snv_mode.bam_readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'snv_mode.bam_readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_indel_mode(self):
@@ -201,7 +294,15 @@ def test_indel_mode(self):
         ]
         vcf_readcount_annotator.main(command)
 
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'indel_mode.bam_readcount.vcf'), os.path.join(temp_path.name, 'input.readcount.vcf')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf'),
+                os.path.join(self.test_data_dir, 'indel_mode.bam_readcount.vcf'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'indel_mode.bam_readcount.vcf'),
+            os.path.join(temp_path.name, 'input.readcount.vcf')
+        ))
         temp_path.cleanup()
 
     def test_complex_indel(self):
@@ -215,7 +316,15 @@ def test_complex_indel(self):
         ]
         vcf_readcount_annotator.main(command)
 
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'complex_indel.readcount.vcf.gz'), os.path.join(temp_path.name, 'input.readcount.vcf.gz')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf.gz'),
+                os.path.join(self.test_data_dir, 'complex_indel.readcount.vcf.gz'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'complex_indel.readcount.vcf.gz'),
+            os.path.join(temp_path.name, 'input.readcount.vcf.gz')
+        ))
         temp_path.cleanup()
 
     def test_mnp(self):
@@ -229,5 +338,13 @@ def test_mnp(self):
         ]
         vcf_readcount_annotator.main(command)
 
-        self.assertTrue(cmp(os.path.join(self.test_data_dir, 'mnp.readcount.vcf.gz'), os.path.join(temp_path.name, 'input.readcount.vcf.gz')))
+        if self.REGENERATE_TEST_DATA:
+            shutil.copy(
+                os.path.join(temp_path.name, 'input.readcount.vcf.gz'),
+                os.path.join(self.test_data_dir, 'mnp.readcount.vcf.gz'),
+            )
+        self.assertTrue(cmp(
+            os.path.join(self.test_data_dir, 'mnp.readcount.vcf.gz'),
+            os.path.join(temp_path.name, 'input.readcount.vcf.gz')
+        ))
         temp_path.cleanup()

From d19f75c06f4cf7c7416103c4f6fb2e9f7a8e7e1d Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Fri, 30 Jan 2026 09:52:35 -0600
Subject: [PATCH 2/3] Add support for Python 3.12

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 11cf0ff..0f6a09f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v2

From fd59b98f242ed461584402d224de4cb45367b0d2 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Fri, 30 Jan 2026 10:32:29 -0600
Subject: [PATCH 3/3] Switch from deprecated distutils function to
 distutils-strtobool package

---
 setup.py                                       | 1 +
 tests/test_ref_transcript_mismatch_reporter.py | 2 +-
 tests/test_vcf_expression_annotator.py         | 2 +-
 tests/test_vcf_genotype_annotator.py           | 2 +-
 tests/test_vcf_info_annotator.py               | 2 +-
 tests/test_vcf_readcount_annotator.py          | 2 +-
 6 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index b5a6391..0007c1e 100644
--- a/setup.py
+++ b/setup.py
@@ -21,6 +21,7 @@
         'pandas',
         'gtfparse==1.3.0',
         'testfixtures',
+        'distutils-strtobool',
     ],
     classifiers=[
         'Development Status :: 5 - Production/Stable',
diff --git a/tests/test_ref_transcript_mismatch_reporter.py b/tests/test_ref_transcript_mismatch_reporter.py
index 3912e5a..685ae79 100644
--- a/tests/test_ref_transcript_mismatch_reporter.py
+++ b/tests/test_ref_transcript_mismatch_reporter.py
@@ -11,7 +11,7 @@
 from io import StringIO
 from unittest.mock import patch
 import shutil
-from distutils.util import strtobool
+from strtobool import strtobool
 
 class RefTranscriptMismatchReporterTests(unittest.TestCase):
     @classmethod
diff --git a/tests/test_vcf_expression_annotator.py b/tests/test_vcf_expression_annotator.py
index c53ea1f..91a8b1b 100644
--- a/tests/test_vcf_expression_annotator.py
+++ b/tests/test_vcf_expression_annotator.py
@@ -8,7 +8,7 @@
 import logging
 from testfixtures import LogCapture, StringComparison as S
 import shutil
-from distutils.util import strtobool
+from strtobool import strtobool
 
 class VcfExpressionAnnotatorTests(unittest.TestCase):
     @classmethod
diff --git a/tests/test_vcf_genotype_annotator.py b/tests/test_vcf_genotype_annotator.py
index c029ba9..670ae9d 100644
--- a/tests/test_vcf_genotype_annotator.py
+++ b/tests/test_vcf_genotype_annotator.py
@@ -6,7 +6,7 @@
 import tempfile
 from filecmp import cmp
 import shutil
-from distutils.util import strtobool
+from strtobool import strtobool
 
 class VcfGenotypeAnnotatorTests(unittest.TestCase):
     @classmethod
diff --git a/tests/test_vcf_info_annotator.py b/tests/test_vcf_info_annotator.py
index 675c481..d1d1264 100644
--- a/tests/test_vcf_info_annotator.py
+++ b/tests/test_vcf_info_annotator.py
@@ -6,7 +6,7 @@
 import tempfile
 from filecmp import cmp
 import shutil
-from distutils.util import strtobool
+from strtobool import strtobool
 
 class VcfInfoAnnotatorTests(unittest.TestCase):
     @classmethod
diff --git a/tests/test_vcf_readcount_annotator.py b/tests/test_vcf_readcount_annotator.py
index 0ed5cb9..2dda661 100644
--- a/tests/test_vcf_readcount_annotator.py
+++ b/tests/test_vcf_readcount_annotator.py
@@ -9,7 +9,7 @@
 import logging
 from testfixtures import LogCapture, StringComparison as S
 import shutil
-from distutils.util import strtobool
+from strtobool import strtobool
 
 class VcfReadcountAnnotatorTests(unittest.TestCase):
     @classmethod