Mercurial > repos > plus91-technologies-pvt-ltd > softsearch

comparison 2.4/script/Subset_targets.sh @ 16:8eb7d93f7e58 draft

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author plus91-technologies-pvt-ltd
date Sat, 31 May 2014 11:23:36 -0400
parents e3609c8714fb
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15:da93b6f4d684 16:8eb7d93f7e58
1 #!/bin/sh
2 #$ -V
3 #$ -cwd
4 #$ -q 1-day
5 #$ -m ae
6 #$ -M hart.steven@mayo.edu
7 #$ -l h_vmem=1G
8 #$ -l h_stack=10M
9 BAM=$1
10 TARGET_BED=$2
11 SAMPLE_NUMBER=$3
12
13 #cat $HEADER > out.${SAMPLE_NUMBER}.sam
14 samtools view -L $TARGET_BED $BAM|
15 perl -ane '
16 next if ($F[10]=~/#/);
17 $minSize=1000;
18 if( $F[1] & 8 || $F[1] & 4 || $F[8] == 0 || abs($F[8]) > $minSize || $F[5] =~/S/){
19 $rName=join("","@",@F[0]);
20 print join ("\n",$rName,$F[9],"+",@F[10])."\n";
21 };
22 ' >> out.${SAMPLE_NUMBER}.fq
23 echo "Done with $BAM `date`"