|
0
|
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`"
|
