BEAR Applications

WhatsHap 0.18-foss-2019a-Python-3.7.2

There is a newer version of WhatsHap

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

Accessing WhatsHap 0.18-foss-2019a-Python-3.7.2

To load the module for WhatsHap 0.18-foss-2019a-Python-3.7.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load WhatsHap/0.18-foss-2019a-Python-3.7.2

BEAR Apps Version

2019a

Architectures

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.

Extensions

• pyfaidx 0.5.5.2
• PyVCF 0.6.8
• WhatsHap 0.18
• xopen 0.7.3

More Information

For more information visit the WhatsHap website.

Dependencies

This version of WhatsHap has a direct dependency on: Biopython/1.73-foss-2019a foss/2019a networkx/2.3-foss-2019a-Python-3.7.2 Pysam/0.15.2-foss-2019a Python/3.7.2-GCCcore-8.2.0

Other Versions

These versions of WhatsHap 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.

Last modified on 22nd July 2019