pybedtools.bedtool.BedTool.multi_bam_coverage

BedTool.multi_bam_coverage(*args, **kwargs)

Wraps bedtools multicov.

Pass a list of sorted and indexed BAM files as bams

For convenience, the file or stream this BedTool points to is implicitly passed as the -bed argument to multiBamCov

Original BEDTools help::

Tool:    bedtools multicov (aka multiBamCov)
Version: v2.31.1
Summary: Counts sequence coverage for multiple bams at specific loci.

Usage:   bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>

Options: 
        -bams   The bam files.

        -bed    The bed file.

        -split  Treat "split" BAM or BED12 entries as distinct BED intervals.

        -s      Require same strandedness.  That is, only report hits in B
                that overlap A on the **same** strand.
                - By default, overlaps are reported without respect to strand.

        -S      Require different strandedness.  That is, only report hits in B
                that overlap A on the **opposite** strand.
                - By default, overlaps are reported without respect to strand.

        -f      Minimum overlap required as a fraction of each -bed record.
                - Default is 1E-9 (i.e., 1bp).
                - FLOAT (e.g. 0.50)

        -r      Require that the fraction overlap be reciprocal for each -bed and B.
                - In other words, if -f is 0.90 and -r is used, this requires
                  that B overlap 90% of each -bed and the -bed record **also** overlaps 90% of B.

        -q      Minimum mapping quality allowed. Default is 0.

        -D      Include duplicate reads.  Default counts non-duplicates only

        -F      Include failed-QC reads.  Default counts pass-QC reads only

        -p      Only count proper pairs.  Default counts all alignments with
                MAPQ > -q argument, regardless of the BAM FLAG field.