- BedTool.igv(*args, **kwargs)¶
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
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.