There is a newer version of BEDToolsThe 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.
Accessing BEDTools 2.29.2-GCC-8.3.0
To load the module for BEDTools 2.29.2-GCC-8.3.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load BEDTools/2.29.2-GCC-8.3.0
BEAR Apps Version
EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell
The listed architectures consist of two part: OS-CPU.
- BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
- BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.
For more information visit the BEDTools website.
This version of BEDTools has a direct dependency on: BamTools/2.5.1-GCC-8.3.0 bzip2/1.0.8-GCCcore-8.3.0 GCC/8.3.0 XZ/5.2.4-GCCcore-8.3.0 zlib/1.2.11-GCCcore-8.3.0
This version of BEDTools is a direct dependent of: funannotate/1.8.1-foss-2019b-Python-2.7.16 funannotate/1.8.1-foss-2019b-Python-3.7.4 pybedtools/0.8.1-foss-2019b
These versions of BEDTools are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
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Last modified on 23rd September 2020