pybedtools.bedtool.BedTool.tag_bam

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

Wraps bedtools tag.

files and labels should lists of equal length.

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

Original BEDTools help::

Tool:    bedtools tag (aka tagBam)
Version: v2.30.0
Summary: Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files
         on the intervals in -i.

Usage:   bedtools tag [OPTIONS] -i <BAM> -files FILE1 .. FILEn  -labels LAB1 .. LABn

Options: 
        -s      Require overlaps on the same strand.  That is, only tag alignments that have the same
                strand as a feature in the annotation file(s).

        -S      Require overlaps on the opposite strand.  That is, only tag alignments that have the opposite
                strand as a feature in the annotation file(s).

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

        -tag    Dictate what the tag should be. Default is YB.
                - STRING (two characters, e.g., YK)

        -names  Use the name field from the annotation files to populate tags.
                By default, the -labels values are used.

        -scores Use the score field from the annotation files to populate tags.
                By default, the -labels values are used.

        -intervals      Use the full interval (including name, score, and strand) to populate tags.
                        Requires the -labels option to identify from which file the interval came.