- BedTool.bedpe_to_bam(*args, **kwargs)¶
For convenience, the file or stream this BedTool points to is implicitly passed as the
There are two alternatives for supplying a genome. Use
g="genome.filename"if you have a genome’s chrom sizes saved as a file. This is the what BEDTools expects when using it from the command line. Alternatively, use the
genome="hg19") to use chrom sizes for that assembly without having to manage a separate file. The
genomeargument triggers a call
pybedtools.chromsizes, so see that method for more details.
Original BEDTools help::
Tool: bedtools bedpetobam (aka bedpeToBam) Version: v2.30.0 Summary: Converts feature records to BAM format. Usage: bedpetobam [OPTIONS] -i <bed/gff/vcf> -g <genome> Options: -mapq Set the mappinq quality for the BAM records. (INT) Default: 255 -ubam Write uncompressed BAM output. Default writes compressed BAM. Notes: (1) BED files must be at least BED4 to create BAM (needs name field).