Difference between revisions of "BEDTools"
Moskalenko (talk | contribs) m (Text replace - "<!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in template calls Required variables: app - lowercase name of the application e.g. "amber" url - url of the software page (project, company prod) |
Moskalenko (talk | contribs) m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "") |
||
| Line 10: | Line 10: | ||
|{{#vardefine:intel|}} <!-- E.g. "11.1" --> | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | ||
| − | + | ||
| − | |||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
Revision as of 17:52, 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.
Required Modules
Serial
- bedtools
System Variables
- HPC_{{#uppercase:bedtools}}_DIR - installation directory
- HPC_BEDTOOLS_BIN - the bin directory
- HPC_BEDTOOLS_DATA - BEDTools data directory
- HPC_BEDTOOLS_GENOMES - BEDTools genomes directory
- HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory