Category
Genomic Interval Manipulation
Usage
bedtools igv [OPTIONS] -i <bed/gff/vcf>
Manual
This tool is part of the bedtools suite.
The tool print out a batch script that are meant to be run from within IGV, and unless you use the -sess option, it is assumed that prior to running the script, you've loaded the proper genome and tracks.
Required arguments
- -i <string>: Intervals stored in a bed/gff/vcf file that you want to capture in IGV.
Options
- -path: The full path to which the IGV snapshots should be written. (STRING) Default: ./.
- -sess <string>: The full path to an existing IGV session file to be loaded prior to taking snapshots. Default is for no session to be loaded.
- -sort <string>: The type of BAM sorting you would like to apply to each image. Options are: 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 not collapse.
- -name: Use the "name" field (column 4) for each image's filename. Default is to use the "chr:start-pos.ext".
- -slop <integer>: Number of flanking base pairs on the left and right of the image. (INT) Default: 0.
- -img <string>: The type of image to be created. Options are: png, eps, svg. Default is png.
Example
Create a batch script
bedtools igv -i test.bed > test.bs
File formats this tool works with
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