pybedtools.bedtool.BedTool.igv

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

Wraps bedtools igv.

The resulting BedTool will have a new attribute igv_script. This attribute is a temp filename containing the IGV script.

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

Original BEDTools help::

Tool:    bedtools igv (aka bedToIgv)
Version: v2.30.0
Summary: Creates a batch script to create IGV images 
         at each interval defined in a BED/GFF/VCF file.

Usage:   bedtools igv [OPTIONS] -i <bed/gff/vcf>

Options: 
        -path   The full path to which the IGV snapshots should be written.
                (STRING) Default: ./

        -sess   The full path to an existing IGV session file to be 
                loaded prior to taking snapshots.

                (STRING) Default is for no session to be loaded.

        -sort   The type of BAM sorting you would like to apply to each image. 
                Options: base, position, strand, quality, sample, and readGroup
                Default is to apply no sorting at all.

        -clps   Collapse the aligned reads prior to taking a snapshot. 
                Default is to no collapse.

        -name   Use the "name" field (column 4) for each image's filename. 
                Default is to use the "chr:start-pos.ext".

        -slop   Number of flanking base pairs on the left & right of the image.
                - (INT) Default = 0.

        -img    The type of image to be created. 
                Options: png, eps, svg
                Default is png.

Notes: 
        (1)  The resulting script is meant to be run from within IGV.
        (2)  Unless you use the -sess option, it is assumed that prior to 
                running the script, you've loaded the proper genome and tracks.