bam2wig.py¶

Convert a BAM file into wiggle format. The BAM file must be sorted and indexed. SAM format is not supported.

Usage¶

bam2wig.py -i input.bam -s chrom.sizes -o output_prefix

Options¶

Option	Description	Default
`-i`, `--input-file`	Alignment file in BAM format (sorted, indexed)	Required
`-s`, `--chromSize`	Chromosome size file (tab-separated: chrom, size)	Required
`-o`, `--out-prefix`	Prefix of output wiggle file(s)	Required
`-t`, `--wigsum`	Normalize to this wigsum (e.g., 1000000000 for 10M 100nt reads)	None
`-u`, `--skip-multi-hits`	Skip non-uniquely mapped reads	Off
`-d`, `--strand`	Strand rule: "1++,1--,2+-,2-+" or "1+-,1-+,2++,2--" or "none"	None
`-q`, `--mapq`	Minimum mapping quality for "uniquely mapped"	30

Output¶

Generates both wiggle (.wig) and BigWig (.bw) files. If strand-specific, produces separate Forward and Reverse files for each format. BigWig files are written natively via pyBigWig — the external wigToBigWig tool is no longer required.