create_browser_track: BED file generation for UCSC and Ensembl genome browsers.

In LDExplorer: Efficient Whole-Genome LD Based Haplotpe Block Recognition

Description

Function transforms mig ouptut file with haplotype blocks into BED format. The BED format allows to visualize haplotype blocks in UCSC and Ensembl genome browsers. The blocks are colored based on haplotype diversity within them: higher red color intensity corresponds to the lower diversity.

Usage

	create_browser_track(input_file, output_file, chromosome, strand, track_name = "", track_desc = "")

Arguments

input_file	The name of the input file with haplotype blocks generated by mig.
output_file	The name of the output BED file.
chromosome	The chromosome name (e.g. chr3, chrY, chr2_random).
strand	The strand: "+" or "-".
track_name	The name of the track, which will be depicted in genome browser.
track_desc	The short description of the track.

Author(s)

Daniel Taliun, Johann Gamper, Cristian Pattaro

LDExplorer documentation built on May 2, 2019, 5:54 p.m.