From 4fe8bcaf7941fdb8034a6635b0c4fa5d25d93d60 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 24 Feb 2018 08:40:44 -0600
Subject: [PATCH] adding updates formatting
---
alignment/markdups.sh | 2 +-
variants/germline_vc.sh | 2 +-
variants/somatic_vc.sh | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 13822b7..6338711 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -39,7 +39,7 @@ module load picard/2.10.3 samtools/1.6
if [ $algo == 'sambamba' ]
then
module load speedseq/20160506
- sambamba markdup -t $SLURM_CPUS_ON_NODE -r ${sbam} ${pair_id}.dedup.bam
+ sambamba markdup -t $SLURM_CPUS_ON_NODE ${sbam} ${pair_id}.dedup.bam
elif [ $algo == 'samtools' ]
then
module load samtools/1.6
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index 6fe2363..970bd01 100644
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -112,7 +112,7 @@ then
else
mode="--exome"
fi
- module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+ module load strelka/2.9.0 samtools/1.6 manta/1.3.1 snpeff/4.3q vcftools/0.1.14
mkdir manta strelka
gvcflist=''
for i in *.bam; do
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index fe274ef..585d670 100644
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -83,7 +83,7 @@ source /etc/profile.d/modules.sh
if [ $algo == 'strelka2' ]
then
- module load strelka/2.8.3 samtools/1.6 manta/1.2.0 snpeff/4.3q vcftools/0.1.14
+ module load strelka/2.9.0 samtools/1.6 manta/1.3.1 snpeff/4.3q vcftools/0.1.14
mkdir manta strelka
configManta.py --normalBam ${mnormal} --tumorBam ${mtumor} --referenceFasta ${reffa} --runDir manta
manta/runWorkflow.py -m local -j 8
--
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