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Commit 68aac6f3 authored by Brandi Cantarel's avatar Brandi Cantarel
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update biohpc var

parent 900cb6c3
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Tags version_1.0.2
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with 5 additions and 2 deletions
variants/germline_vc.sh
+ 5
− 2
View file @ 68aac6f3
...@@ -83,12 +83,15 @@ then ...@@ -83,12 +83,15 @@ then
bgzip ${pair_id}.sam.vcf bgzip ${pair_id}.sam.vcf
elif [[ $algo == 'fb' ]] elif [[ $algo == 'fb' ]]
then then
paropt="--delay 1 --jobs 0 --memfree 2G"
if [[ -z $isdocker ]] if [[ -z $isdocker ]]
then then
module load freebayes/gcc/1.2.0 parallel/20150122 module load freebayes/gcc/1.2.0 parallel/20150122
paropt="--delay 2 -j $NPROC" paropt="--delay 2 -j $NPROC"
else fi
paropt="--delay 1 --jobs 0 --memfree 2G" if [[ -n $biohpc ]]
then
paropt="--delay 2 -j $NPROC"
fi fi
bamlist='' bamlist=''
for i in *.bam; do for i in *.bam; do
......
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