Difference between revisions of "BEDTools"
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Revision as of 16:29, 10 August 2012
Description
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.
- Intersecting two BED files in search of overlapping features.
- Culling/refining/computing coverage for BAM alignments based on genome features.
- Merging overlapping features.
- Screening for paired-end (PE) overlaps between PE sequences and existing genomic features.
- Calculating the depth and breadth of sequence coverage across defined "windows" in a genome.
- Screening for overlaps between "split" alignments and genomic features.
The fact that all of the BEDTools accept input from “standard input (stdin)” allows one to “stream / pipe” several commands together to facilitate more complicated analyses. Also, the tools allow fine control over how output is reported. Most recently, I have added support for sequence alignments in BAM ([1]) format, as well as for features in VCF and GFF, as well as “blocked” BED format. The tools are quite fast and typically finish in a matter of a few seconds, even for large datasets. Upstream documentation for bedtools.
Execution Environment and Modules
To use bedtools with the environment modules system at HPC the following commands are available:
Get module information for bedtools:
$module spider bedtools
Load the default application module:
$module load bedtools
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_BEDTOOLS_DIR - directory where bedtools is located.
- HPC_BEDTOOLS_BIN - the bin directory
- HPC_BEDTOOLS_DATA - BEDTools data directory
- HPC_BEDTOOLS_GENOMES - BEDTools genomes directory
- HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory