bedtools links

Reference Code backup Executable files

Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.

Category

Genomic Interval Manipulation

Usage

bedtools links [OPTIONS] -i <bed/gff/vcf> > out.html

Manual

This tool is part of the bedtools suite and it's also known as linksBed.

Related tools: bedtools igv

Required arguments

  • -i input_file: Path to the input feature file in BED, GFF, or VCF format.

Options

  • -base URL: The browser basename. Default: http://genome.ucsc.edu
  • -org organism: The organism. Default: human
  • -db build: The genome build or version to use for generating the links. Default: hg18

Examples

By default, the links created will point to human (hg18) UCSC browser. If you have a local mirror, you can override this behavior by supplying the -base, -org, and -db options.
In the following example, bedtools links creates links to UCSC genome browser for regions (hg38) in test.bed:

bedtools links -i test.bed -db hg38 > test.html

And the content in the output html file looks like the following:

BED Entries from: stdin
chr1:100036040-100038153
chr1:100037361-100039474

File formats this tool works with
BEDGFFGTFVCF

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