Convert BAM to BigWig coverage (useful for visualization in UCSC Browser)

bam2bw.sh

#!/bin/bash
# generate coverage profiles
vis="./vis"
chromsizes="foo.chrom.sizes"
genomeCoverageBed=`which genomeCoverageBed`
bedGraphToBigWig=`which bedGraphToBigWig`

if ! [ -d "$vis" ];
then
mkdir -p $vis
echo "created $vis"
fi

set -x
for BAM in $(ls *.bam)
do
        $genomeCoverageBed -ibam $BAM -bg -g $chromsizes > $vis/$BAM.bg
        $bedGraphToBigWig $vis/$BAM.bg $chromsizes $vis/$BAM.bw
done
set +x