Bedops

Overview

Bedops: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.

Using

Use the module name bedopsto discover versions available and to load the application.

Beartooth

Version 2.4.40 on Beartooth, contains the following commands:

bam2bed                 bam2starch_sge    convert2bed  gvf2starch   sam2starch                 starchcluster_slurm                 update-sort-bed-starch-slurm
bam2bed_gnuParallel     bam2starch_slurm  gff2bed      psl2bed      sort-bed                   starch-diff                         vcf2bed
bam2bed_sge             bedextract        gff2starch   psl2starch   starch                     starchstrip                         vcf2starch
bam2bed_slurm           bedmap            gtf2bed      rmsk2bed     starchcat                  unstarch                            wig2bed
bam2starch              bedops            gtf2starch   rmsk2starch  starchcluster_gnuParallel  update-sort-bed-migrate-candidates  wig2starch
bam2starch_gnuParallel  closest-features  gvf2bed      sam2bed      starchcluster_sge          update-sort-bed-slurm