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