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PoC capice wgs update #783

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PoC capice wgs update #783

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74f4f12
Update vip annotations for new capice
Timniem Mar 2, 2026
de5a37c
fix: added numberType to metadata.json
Timniem Mar 3, 2026
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2 changes: 1 addition & 1 deletion config/nxf_vcf.config
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ params {
vep_plugin_spliceai_snv = "${VIP_DIR_DATA}/resources/GRCh38/spliceai_scores.masked.snv.hg38.vcf.gz"
vep_plugin_utrannotator = "${VIP_DIR_DATA}/resources/GRCh38/uORF_5UTR_PUBLIC.txt"
vep_plugin_vkgl = "${VIP_DIR_DATA}/resources/GRCh38/vkgl_consensus_20250701.tsv"
vep_plugin_alphscore = "${VIP_DIR_DATA}/resources/GRCh38/AlphScore_final_20230825_stripped_GRCh38.tsv.gz"
vep_plugin_amscore = "${VIP_DIR_DATA}/resources/capice/add_data/AlphaMissense_hg38.tsv.gz"
vep_plugin_ncer = "${VIP_DIR_DATA}/resources/GRCh38/GRCh38_ncER_perc.bed.gz"
vep_plugin_green_db = "${VIP_DIR_DATA}/resources/GRCh38/GRCh38_GREEN-DB.bed.gz"
vep_plugin_fathmm_MKL_scores = "${VIP_DIR_DATA}/resources/GRCh38/GRCh38_FATHMM-MKL_NC.tsv.gz"
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2 changes: 1 addition & 1 deletion modules/vcf/annotate.nf
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Expand Up @@ -36,7 +36,7 @@ process annotate {
fathmmMKLScoresPath = params.vcf.annotate[assembly].vep_plugin_fathmm_MKL_scores
reMMScoresPath = params.vcf.annotate[assembly].vep_plugin_ReMM_scores
capiceModelPath = params.vcf.annotate[assembly].capice_model
alphScorePath = params.vcf.annotate[assembly].vep_plugin_alphscore
amScorePath = params.vcf.annotate[assembly].vep_plugin_amscore
strangerCatalog = params.vcf.annotate[assembly].stranger_catalog

areProbandHpoIdsIndentical = areProbandHpoIdsIndentical(meta.project.samples)
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15 changes: 13 additions & 2 deletions modules/vcf/templates/annotate.sh
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Expand Up @@ -78,8 +78,16 @@ capice_vep() {
args+=("--dir_plugins" "!{params.vcf.annotate.vep_plugin_dir}")
args+=("--plugin" "SpliceAI,snv=!{vepPluginSpliceAiSnvPath},indel=!{vepPluginSpliceAiIndelPath}")
args+=("--plugin" "Grantham")
args+=("--plugin" "NMD")
args+=("--plugin" "pLI_LOEUF")
args+=("--plugin" "Downstream")
args+=("--plugin" "UTRannotator,!{vepPluginUtrAnnotatorPath}")
args+=("--custom" "!{vepCustomPhyloPPath},phyloP,bigwig,exact,0")
args+=("--plugin" "gnomAD,!{vepPluginGnomAdPath}")
args+=("--plugin" "AlphaMissense,file=!{amScorePath}")
args+=("--plugin" "ncER,!{vepPluginNcerPath}")
args+=("--plugin" "FATHMM_MKL_NC,!{fathmmMKLScoresPath}")
args+=("--plugin" "ReMM,!{reMMScoresPath}")

${CMD_VEP} "${args[@]}"
}
Expand Down Expand Up @@ -178,6 +186,9 @@ vep() {
args+=("--hgvs")
args+=("--dir_plugins" "!{params.vcf.annotate.vep_plugin_dir}")
args+=("--plugin" "Grantham")
args+=("--plugin" "NMD")
args+=("--plugin" "pLI_LOEUF")
args+=("--plugin" "Downstream")
if [ "!{vepPluginSpliceAiEnabled}" = true ]; then
args+=("--plugin" "SpliceAI,snv=!{vepPluginSpliceAiSnvPath},indel=!{vepPluginSpliceAiIndelPath}")
args+=("--plugin" "Capice,${capiceOutputPath}")
Expand Down Expand Up @@ -206,8 +217,8 @@ vep() {
# when you change the field also update the empty file header in this file
args+=("--plugin" "AnnotSV,!{vcf}.tsv,!{params.vcf.annotate.vep_plugin_annotsv_columns}")
fi
if [ -n "!{alphScorePath}" ]; then
args+=("--plugin" "AlphScore,!{alphScorePath}")
if [ -n "!{amScorePath}" ]; then
args+=("--plugin" "AlphaMissense,file=!{amScorePath}")
fi
if [ -n "!{vepPluginNcerPath}" ]; then
args+=("--plugin" "ncER,!{vepPluginNcerPath}")
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13 changes: 10 additions & 3 deletions resources/field_metadata.json
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Expand Up @@ -88,9 +88,9 @@
"numberCount": 1,
"type": "INTEGER"
},
"ALPHSCORE": {
"label": "AlphScore",
"description": "AlphScore pathogenicity score for missense variants",
"am_pathogenicity": {
"label": "AmScore",
"description": "AlphaMissense pathogenicity score for missense variants",
"numberType": "NUMBER",
"numberCount": 1,
"type": "FLOAT"
Expand Down Expand Up @@ -570,6 +570,13 @@
}
}
},
"LOEUF_gene_value": {
"label": "LOEUF",
"numberType": "NUMBER",
"description": "An Ensembl VEP plugin that adds the loss-of-function observed/expected upper bound fraction (LOEUF) score ",
"type": "FLOAT",
"numberCount":1
},
"mitoTip_Quartile": {
"label": "MitoTIP Quartile",
"description": "MitoTIP score quartile",
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