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.
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 - executable directory
- HPC_BEDTOOLS_DATA - data directory
- HPC_BEDTOOLS_GENOMES - genomes directory
- HPC_BEDTOOLS_SCRIPTS - genomes directory