bam-to-bedGraph.sh

#!/usr/bin/env bash

source ~/.config/extpaths # For samtools

set -e
set -u

n=0

for bam in $*; do
    out="${bam%.bam}.bgr.gz"
    let n=n+1

    echo "$bam    $out"
    bsub -J test-$n "
        echo 'track type=bedGraph' > \"$out\"
        samtools view \"$bam\" | while read qname flag chr pos mapq cigar rnext pnext tlen seq; do
            let start=\$pos-1
            end=\$pos+\${#seq}
            echo \"\$chr	\$start	\$end\"
        done | gzip -c >> \"$out\""
done