From 9975bc74907d2fe9577829d035f512dd128f3273 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 23 Jan 2020 15:02:45 -0600
Subject: [PATCH] add reference genome
---
variants/norm_annot.sh | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/variants/norm_annot.sh b/variants/norm_annot.sh
index a9e869a..1f05c4e 100755
--- a/variants/norm_annot.sh
+++ b/variants/norm_annot.sh
@@ -15,6 +15,7 @@ do
case $opt in
p) pair_id=$OPTARG;;
v) vcf=$OPTARG;;
+ r) index_path=$OPTARG;;
h) usage;;
esac
done
@@ -25,6 +26,15 @@ baseDir="`dirname \"$0\"`"
source /etc/profile.d/modules.sh
module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q
+if [[ -a "${index_path}/genome.fa" ]]
+then
+ reffa="${index_path}/genome.fa"
+ dict="${index_path}/genome.dict"
+else
+ echo "Missing Fasta File: ${index_path}/genome.fa"
+ usage
+
+fi
perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
bgzip -f ${pair_id}.uniform.vcf
--
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