pybedtools.bedtool.BedTool.bam_to_bed

BedTool.bam_to_bed(*args, **kwargs)[source]

Wraps bedtools bamtobed.

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

Original BEDTools help::

Tool:    bedtools bamtobed (aka bamToBed)
Version: v2.30.0
Summary: Converts BAM alignments to BED6 or BEDPE format.

Usage:   bedtools bamtobed [OPTIONS] -i <bam> 

Options: 
        -bedpe  Write BEDPE format.
                - Requires BAM to be grouped or sorted by query.

        -mate1  When writing BEDPE (-bedpe) format, 
                always report mate one as the first BEDPE "block".

        -bed12  Write "blocked" BED format (aka "BED12"). Forces -split.

                http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1

        -split  Report "split" BAM alignments as separate BED entries.
                Splits only on N CIGAR operations.

        -splitD Split alignments based on N and D CIGAR operators.
                Forces -split.

        -ed     Use BAM edit distance (NM tag) for BED score.
                - Default for BED is to use mapping quality.
                - Default for BEDPE is to use the minimum of
                  the two mapping qualities for the pair.
                - When -ed is used with -bedpe, the total edit
                  distance from the two mates is reported.

        -tag    Use other NUMERIC BAM alignment tag for BED score.
                - Default for BED is to use mapping quality.
                  Disallowed with BEDPE output.

        -color  An R,G,B string for the color used with BED12 format.
                Default is (255,0,0).

        -cigar  Add the CIGAR string to the BED entry as a 7th column.