pybedtools.contrib.bigwig.bam_to_bigwig(bam, genome, output, scale=False)[source]

Given a BAM file bam and assembly genome, create a bigWig file scaled such that the values represent scaled reads – that is, reads per million mapped reads.

(Disable this scaling step with scale=False; in this case values will indicate number of reads)

Assumes that bedGraphToBigWig from UCSC tools is installed; see for more details on the format.