From 16f5c7026728ed63d0a8ad567f85e0db5b35aa6f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 2 May 2018 14:46:46 -0500
Subject: [PATCH] add repeat type
---
variants/annotvcf.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 1ca2a78..21c869e 100644
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -35,7 +35,8 @@ 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}
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
+ 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
tabix ${pair_id}.annot.vcf.gz
else
if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCm38' ]]
--
GitLab