Extract properly-paired reads and their mates (ie flags 99/147/163/83) from paired-end BAM files

extract_pp.sh

#!/bin/bash
samtools=`which samtools`
bn=$(basename $1 .bam)

echo processing $bn
$samtools view -h -b -f99  $1 > $bn.flag99.bam
$samtools view -h -b -f147 $1 > $bn.flag147.bam
$samtools view -h -b -f163 $1 > $bn.flag163.bam
$samtools view -h -b -f83  $1 > $bn.flag83.bam

echo merging tmp BAM files
$samtools merge $bn.uns.pp.bam $bn.flag99.bam $bn.flag147.bam $bn.flag163.bam $bn.flag83.bam

echo sorting final BAM file
$samtools sort $bn.uns.pp.bam $bn.pp

echo cleaning up
rm $bn.flag99.bam
rm $bn.flag147.bam
rm $bn.flag163.bam
rm $bn.flag83.bam
rm $bn.uns.pp.bam