From ed054149c9d5e35d62ead0d92b9c6a7e6c1caa6c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 9 Jul 2018 09:03:22 -0500
Subject: [PATCH] adding union
---
variants/union.sh | 16 ++++++++++++----
1 file changed, 12 insertions(+), 4 deletions(-)
diff --git a/variants/union.sh b/variants/union.sh
index 204b550..1a85d4f 100755
--- a/variants/union.sh
+++ b/variants/union.sh
@@ -9,11 +9,12 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:p:h opt
+while getopts :r:d:p:h opt
do
case $opt in
r) index_path=$OPTARG;;
p) pair_id=$OPTARG;;
+ d) dir=$OPTARG;;
h) usage;;
esac
done
@@ -21,15 +22,22 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
shift $(($OPTIND -1))
baseDir="`dirname \"$0\"`"
+echo $pair_id $index_path $dir
+
+if [[ -z $dir ]]
+then
+dir='.'
+fi
+
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q
HS=*.hotspot.vcf.gz
-list1=`ls *vcf.gz|grep -v hotspot`
-list2=`ls *vcf.gz|grep -v hotspot`
+list1=`ls ${dir}/*vcf.gz|grep -v hotspot`
+list2=`ls ${dir}/*vcf.gz|grep -v hotspot`
varlist=''
calllist=''
-for i in *.vcf.gz; do
+for i in ${dir}/*.vcf.gz; do
if [[ $i == $HS ]]
then
bcftools norm -m - -O z -o hotspot.norm.vcf.gz $i
--
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