From 60f7ac36cb3239707f5f645f841b61f7733e8c3e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 19 Sep 2018 10:56:27 -0500
Subject: [PATCH] gatk/3.7 -> gatk/3.8
---
variants/gatkrunner.sh | 2 +-
variants/germline_vc.sh | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index 2dcd150..51b0237 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -57,7 +57,7 @@ else
fi
source /etc/profile.d/modules.sh
-module load gatk/3.7 samtools/1.6
+module load gatk/3.8 samtools/1.6
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
if [[ $algo == 'gatkbam_rna' ]]
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 9b04124..a2c2c55 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -84,7 +84,7 @@ then
vcf-annotate -n --fill-type ssvar.vcf.gz| bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.ssvar.vcf.gz -
elif [[ $algo == 'gatk' ]]
then
- module load gatk/3.7
+ module load gatk/3.8
gvcflist=''
for i in *.bam; do
cut -f 1 ${index_path}/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Djava.io.tmpdir=./ -Xmx32g -jar $GATK_JAR -R ${reffa} -D ${dbsnp} -T HaplotypeCaller -stand_call_conf 10 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -I $i -o ${i}.{}.chr.gatk.g.vcf -nct 2 -L {}"
--
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