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run_manta.sh
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run_manta.sh
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#!/usr/bin/env bash
#henan
data=henan
echo $data
sleep 10
if [ $data == "henan" ]
then
wgstumors=(3A 11A 13A 15A 17A 25A 29A 33A 37A 41A)
wgsnormals=(4A 12A 14A 16A 18A 26A 30A 34A 38A 42A)
bamdir=/fh/scratch/delete30/dai_j/henan
ext=.merged.deduprealigned.bam
for ((i=0;i<${#wgstumors[@]};i++))
do
normalbam=$bamdir/${wgsnormals[$i]}$ext
tumorbam=$bamdir/${wgstumors[$i]}$ext
rundir=/fh/scratch/delete30/dai_j/henan/manta/${wgstumors[$i]}
echo sbatch -n 1 -c 8 /fh/fast/dai_j/CancerGenomics/Tools/wang/SV/manta.sh $normalbam $tumorbam $rundir
sbatch -n 1 -c 8 /fh/fast/dai_j/CancerGenomics/Tools/wang/SV/manta.sh $normalbam $tumorbam $rundir
sleep 1
done
fi
if [ $data == "dulak" ]
then
wgsnormals=(SRR1002719 SRR999433 SRR999687 SRR1000378 SRR1002786 SRR999559 SRR1001730 SRR10018461 SRR1002703 SRR999599 SRR1002792 SRR1001839 SRR9994281 SRR1002710 SRR9995631 SRR1021476)
wgstumors=(SRR1001842 SRR1002713 SRR999423 SRR1001466 SRR1002670 SRR1001823 SRR999489 SRR1002343 SRR1002722 SRR1002656 SRR1002929 SRR999438 SRR1001915 SRR999594 SRR1001868 SRR1001635)
bamdir=/fh/scratch/delete30/dai_j/dulak
ext=.dedup.realigned.recal.bam
for ((i=0;i<${#wgstumors[@]};i++))
do
normalbam=$bamdir/${wgsnormals[$i]}$ext
tumorbam=$bamdir/${wgstumors[$i]}$ext
rundir=/fh/scratch/delete30/dai_j/manta/${wgstumors[$i]}
echo sbatch -n 1 -c 8 /fh/fast/dai_j/CancerGenomics/Tools/wang/SV/manta.sh $normalbam $tumorbam $rundir
sbatch -n 1 -c 8 /fh/fast/dai_j/CancerGenomics/Tools/wang/SV/manta.sh $normalbam $tumorbam $rundir
sleep 1
done
fi