From ae56c421b7e0c9d67e216b614f9af3cd98ee8135 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 9 Mar 2018 15:06:42 -0600
Subject: [PATCH] update annot dbs
---
variants/annotvcf.sh | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 9d7595e..1ca2a78 100644
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -19,7 +19,7 @@ do
h) usage;;
esac
done
-function join_by { local IFS="$1"; shift; echo "$*"; }
+
shift $(($OPTIND -1))
source /etc/profile.d/modules.sh
@@ -33,9 +33,9 @@ fi
if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
then
tabix ${unionvcf}
- bcftools annotate -Oz -a ${index_path}/ExAC.vcf.gz -o ${pair_id}.exac.vcf.gz --columns CHROM,POS,AC_Het,AC_Hom,AC_Hemi,AC_Adj,AN_Adj,AC_POPMAX,AN_POPMAX,POPMAX ${unionvcf}
- tabix ${pair_id}.exac.vcf.gz
- java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.exac.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
+ 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}
+ tabix ${pair_id}.gnomad.vcf.gz
+ java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.gnomad.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
tabix ${pair_id}.annot.vcf.gz
else
if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCm38' ]]
--
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