Add GDA EGT cluster INFO BCF source#103
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Adds the reference "expected" half of the observed-vs-EGT comparison that the popgen-genotyping SNP QC report needs: a sample-less BCF whose INFO carries the EGT cluster geometry from GDA-8v1-0_D1_ClusterFile.egt (GenTrain_Score, Cluster_Sep, N_AA/AB/BB, meanTHETA_*/devTHETA_*, meanR_*/devR_*). * illumina_microarray/extract_egt_info_bcf.sh — standalone bash driver. Runs `bcftools +gtc2vcf` with no `--gtcs` against the canonical GDA-8v1-0 BPM + EGT + GRCh38 fasta, pipes through `norm`, `sort`, `view -G -O b --write-index=csi`. Mirrors the production gtc2vcf invocation in popgen-genotyping. Supports `--upload-only` so the bcftools build can run inside the bcftools:1.23-1 container and the gcloud upload runs from the host. * references.py — new `illumina_microarray_egt_info` Source pointing at gs://cpg-common-test/references/illumina_microarray/egt_info/ with gcs_rsync, mirroring the hail_intervals_hg38 staging pattern. CI will rsync the BCF + CSI into cpg-common-main on merge. Artifact already staged to the test bucket: gs://cpg-common-test/references/illumina_microarray/egt_info/GDA-8v1-0_D1_egt_info.bcf (159 MB, 1,862,364 records) gs://cpg-common-test/references/illumina_microarray/egt_info/GDA-8v1-0_D1_egt_info.bcf.csi (1.4 MB)
joshuamschmidt
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Summary
Adds the reference "expected" half of the observed-vs-EGT comparison for updates to popgen-genotyping SNP QC.
illumina_microarray/extract_egt_info_bcf.sh— standalone bash build script. Runsbcftools +gtc2vcfagainst the GDA-8v1-0 BPM + EGT + GRCh38 fasta with no--gtcs, piping throughnorm,sort, andview -G -O b --write-index=csi. Output:GDA-8v1-0_D1_ClusterFile_info.bcf{,.csi}in--out-dir.illumina_microarray/copy_egt_info_bcf_to_main.sh— minimalgcloud storage cpfromcpg-common-testtocpg-common-main. Run via analysis-runner at--access-level full --dataset common.references.py— addsGDA_8v1_0_D1_ClusterFile_egt_info_bcf{,_index}as keys on the existingillumina_microarraySource (no new Source, notransfer_cmd). The promote script is the transfer mechanism.The output BCF carries the per-variant INFO directly from the EGT cluster file:
GenTrain_Score,Cluster_Sep,N_AA/AB/BB,meanTHETA_AA/AB/BB,devTHETA_AA/AB/BB,meanR_AA/AB/BB,devR_AA/AB/BB(plusALLELE_A/B,FRAC_*,INTENSITY_ONLY,GC, etc.).Sequencing
Staging into the test bucket is a manual
gcloud storage cpstep (no flag on the build script). Canonical staged paths:After merge, run the job to copy the files to main with AR:
Tests
cpg-common-main/references/illumina_microarray/(BPM, EGT, GRCh38 fasta) — 1,862,364 records emitted (1,904,599 BPM total − 3,352 skipped by gtc2vcf − 38,929 reference-mismatch removed bynorm+ 46 multiallelic splits).INFOfields; spot-check record has populated cluster moments.view -Gdid its job.gs://cpg-common-test/references/illumina_microarray/with theClusterFile_infofilenames.copy_egt_info_bcf_to_main.shvia analysis-runner at--access-level fulland confirm BCF + CSI land atgs://cpg-common-main/references/illumina_microarray/.references.tomlgainsillumina_microarray.GDA_8v1_0_D1_ClusterFile_egt_info_bcf{,_index}after the next references-repo CI run.