From dfe396d9dfb12c88fb92635c86c5e8f2e5e2d4fc Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 20 Feb 2019 14:09:52 -0600
Subject: [PATCH] update to if for reference location
---
variants/annotvcf.sh | 6 +++---
variants/cnvkit.sh | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 7bc785b..79f7f2e 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -25,12 +25,12 @@ 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
-if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38/hisat_index' ]]
+if [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38/hisat_index' ]]
then
- index_path='/project/shared/bicf_workflow_ref/GRCh38'
+ index_path='/project/shared/bicf_workflow_ref/human/GRCh38'
fi
-if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
+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 ${unionvcf}
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index 98c3363..ea813fb 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -46,7 +46,7 @@ then
then
normals="${index_path}/UTSWV2.uminormals.cnn"
fi
-elif [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
+elif [[ $capture == '/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/UTSWV2_2.panelplus.bed' ]]
then
normals="${index_path}/panelofnormals.panel1385V2_2.cnn"
targets="${index_path}/panel1385V2-2.cnvkit_"
--
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