From 44e1d679a97d61c5d380629c2a15b1203f74354f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 2 Mar 2019 17:37:48 -0600
Subject: [PATCH] new gnomad version
---
variants/annotvcf.sh | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 1f4d972..22a4488 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -23,7 +23,7 @@ done
shift $(($OPTIND -1))
source /etc/profile.d/modules.sh
-module load python/2.7.x-anaconda bedtools/2.26.0 samtools/1.6 snpeff/4.3q
+module load bedtools/2.26.0 samtools/1.6 snpeff/4.3q
if [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38/hisat_index' ]]
then
@@ -32,8 +32,8 @@ fi
if [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]]
then
- tabix ${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 -f ${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,GNOMAD_HG19_VARIANT -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-downstream -no-upstream -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
@@ -41,7 +41,7 @@ then
else
if [[ $index_path == '/project/shared/bicf_workflow_ref/mouse/GRCm38' ]]
then
- snpeffvers='GRCh38.86'
+ snpeffvers='GRCm38.86'
elif [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh37' ]]
then
snpeffvers='GRCh37.75'
--
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