Difference between revisions of "BEDTools"
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|{{#vardefine:app|bedtools}} | |{{#vardefine:app|bedtools}} | ||
|{{#vardefine:url|http://code.google.com/p/bedtools/}} | |{{#vardefine:url|http://code.google.com/p/bedtools/}} | ||
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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. | 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. | ||
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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 ([http://samtools.sourceforge.net/]) 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. | 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 ([http://samtools.sourceforge.net/]) 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. | ||
[http://code.google.com/p/bedtools/wiki/Usage Upstream documentation] for {{#var:app}}. | [http://code.google.com/p/bedtools/wiki/Usage Upstream documentation] for {{#var:app}}. | ||
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| − | < | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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*HPC_BEDTOOLS_BIN - the bin directory | *HPC_BEDTOOLS_BIN - the bin directory | ||
*HPC_BEDTOOLS_DATA - BEDTools data directory | *HPC_BEDTOOLS_DATA - BEDTools data directory | ||
*HPC_BEDTOOLS_GENOMES - BEDTools genomes directory | *HPC_BEDTOOLS_GENOMES - BEDTools genomes directory | ||
*HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory | *HPC_BEDTOOLS_SCRIPTS - BEDTools scripts directory | ||
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WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Latest revision as of 12:48, 15 August 2022
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.
Environment Modules
Run module spider bedtools to find out what environment modules are available for this application.
System Variables
- HPC_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