bt.igv: Creates a batch script to create IGV images at each interval...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.

Description

Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.

Usage

bt.igv(
  i,
  path = NULL,
  sess = NULL,
  sort = NULL,
  clps = NULL,
  name = NULL,
  slop = NULL,
  img = NULL,
  output = NULL
)

Arguments

i	<bed/gff/vcf>
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.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.