How to get a coverage graph in WIG file format directly from an alignment (BAM)

The following command combines the samtools mpileup tool with command line perl to obtain genomic coverage plot from an alignment in BAM format.

samtools mpileup -BQ0 run.sorted.bam | perl -pe '($c, $start, undef, $depth) = split;if ($c ne $lastC || $start != $lastStart+1) {print "fixedStep chrom=$c start=$start step=1 span=1\n";}$_ = $depth."\n";($lastC, $lastStart) = ($c, $start);' | gzip -c > run.wig.gz

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Last updated on August 09, 2013