From 900cb6c327caa9604560ac29b97560ef120ca20d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 28 Aug 2020 16:06:53 -0500
Subject: [PATCH] add is docker to annot and update AD field for platypus
---
variants/annotvcf.sh | 7 +++++--
variants/uniform_vcf_gt.pl | 1 +
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index c538256..d7626ae 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -23,8 +23,11 @@ done
shift $(($OPTIND -1))
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0 snpeff/4.3q
+if [[ -z $isdocker ]]
+then
+ source /etc/profile.d/modules.sh
+ module load bedtools/2.26.0 snpeff/4.3q
+fi
if [[ $index_path == '/project/shared/bicf_workflow_ref/human/grch38_cloud/rnaref' ]]
then
diff --git a/variants/uniform_vcf_gt.pl b/variants/uniform_vcf_gt.pl
index 85b8e06..d73aad4 100755
--- a/variants/uniform_vcf_gt.pl
+++ b/variants/uniform_vcf_gt.pl
@@ -93,6 +93,7 @@ while (my $line = <VCF>) {
$gtdata{DP} = $gtdata{NR};
$gtdata{AO} = $gtdata{NV};
$gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+ $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
} elsif (exists $gtdata{AO} && exists $gtdata{RO}) {
$gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
$gtdata{DP} = $gtdata{RO};
--
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