From 6196b5de68e2ebc1a4728cdb9e1300bb7a063f44 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 27 Oct 2018 19:10:39 -0500
Subject: [PATCH] new gnomad file
---
variants/annotvcf.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 21c869e..f3d2462 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -33,7 +33,7 @@ fi
if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
then
tabix ${unionvcf}
- bcftools annotate -Oz -a ${index_path}/gnomad.exomes.r2.0.2.HG38.vcf.gz -o ${pair_id}.gnomad.vcf.gz --columns CHROM,POS,AF,AF_raw,AF_POPMAX,POPMAX ${unionvcf}
+ bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
tabix ${pair_id}.gnomad.vcf.gz
bcftools annotate -Oz -a ${index_path}/repeat_regions.bed.gz -o ${pair_id}.repeat.vcf.gz --columns CHROM,FROM,TO,RepeatType -h /project/shared/bicf_workflow_ref/RepeatType.header ${pair_id}.gnomad.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
--
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