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Commit 4fe8bcaf authored by Brandi Cantarel's avatar Brandi Cantarel
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adding updates formatting

parent d8c03da1
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......@@ -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
......
......@@ -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
......
......@@ -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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