Added endpoint for getClinvarVariantsV3

scripts/getClinvarVariantsV3.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+set -euo pipefail
+#
+# getClinvarVariantsV3.sh
+#
+# This is a special version of annotateVariantsVx.sh. Since Clinvar variants 
+# are already annotated and don't have genotypes, they require different
+# steps, more easily accomplished in a separate bash script. The steps are:
+#  1) annotate clinvar variants with gnomad allele frequencies 
+#  2) normalize the variants (i.e. convert to canonical representation)
+#  3) filter the variants via an input arg. For example, return onlyvariants 
+#     that are pathogenic or likely pathogenic.  
+#
+# Example usage:
+# /iobio-gru-backend/scripts/getClinvarVariantsV3.sh \
+#     "https://backend.iobio.io/static/clinvar/GRCh38/clinvar.vcf.gz" \
+#     "https://backend.iobio.io/static/clinvar/GRCh38/clinvar.vcf.gz.tbi" \
+#     "9:1979290-2194624" \
+#     "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" \
+#     "/gru_data/references/GRCh38/Homo_sapiens_assembly38.fasta" \
+#     "GRCh38" \
+#     "true" \
+#     'INFO/CLNSIG="Pathogenic,Likely_pathogenic"'
+
+
+vcfUrl=$1              # vcf url
+tbiUrl=$2              # optional tbi url
+region=$3              # region to extract (e.g. 9:1979290-2194624)
+contigStr=$4           # contigs for header (e.g. chr1,...,chr22,chrX,chrY,chrM  or 1,2,X,Y,M)
+refFastaFile=$5        # reference fasta file
+genomeBuildName=$6     # genome build name (e.g. GRCh38, GRCh37)
+gnomadMergeAnnots=$7   # true to annotate with gnomad, "" to skip
+pathoFilterPhrase=${8} # bcftools filter phrase, e.g. "INFO/CLNSIG=\"Pathogenic,Likely_pathogenic\"" 
+
+
+echo -e "$contigStr" > contigs.txt
+
+tabixVcfArg=$vcfUrl
+if [ -n "${tbiUrl}" ]; then
+    tabixVcfArg="$vcfUrl##idx##$tbiUrl"
+fi
+
+#optional gnomad stage
+gnomadAnnotStage=cat
+if [ "$gnomadMergeAnnots" ]; then
+
+    if [ "$genomeBuildName" == "GRCh38" ]; then
+        toml="/gru_data/annotations/GRCh38/vcfanno_annotate_variants.toml"
+    else
+        toml="/gru_data/annotations/GRCh37/vcfanno_annotate_variants.toml"
+    fi
+    custom_lua="/gru_data/annotations/vcfanno_custom.lua"
+    gnomadAnnotStage="vcfanno --lua $custom_lua $toml /dev/stdin"
+fi
+
+tabix -h $tabixVcfArg $region | \
+    bcftools annotate -h contigs.txt - | \
+    vt normalize -n -r $refFastaFile - | \
+    bcftools filter -i $pathoFilterPhrase - | \
+    $gnomadAnnotStage

src/index.js

@@ -340,6 +340,23 @@ router.post('/getClinvarVariantsV2', async (ctx) => {
     await handle(ctx, 'getClinvarVariantsV2.sh', args, { ignoreStderr: true });
 });
 
+router.post('/getClinvarVariantsV3', async (ctx) => {
+  const params = JSON.parse(ctx.request.body);
+
+  const tbiUrl = params.tbiUrl ? params.tbiUrl : '';
+  const contigStr = genContigFileStr(params.refNames);
+  const regionStr = genRegionsStr(params.regions);
+  const refFastaFile = dataPath(params.refFastaFile);
+  const gnomadMergeAnnots = params.gnomadMergeAnnots ? params.gnomadMergeAnnots : '';
+
+  const args = [
+      params.vcfUrl, tbiUrl, regionStr, contigStr, refFastaFile, 
+      params.genomeBuildName, gnomadMergeAnnots, params.clinSigFilterPhrase
+  ];
+
+  await handle(ctx, 'getClinvarVariantsV3.sh', args, { ignoreStderr: true });
+});
+
 router.post('/annotateVariants', async (ctx) => {
 
     const params = JSON.parse(ctx.request.body);