There is a newer version of Pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

Accessing Pysam

To load the module for Pysam please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load Pysam/

BEAR Apps Version


More Information

For more information visit the Pysam website.


This version of Pysam has a direct dependency on: cURL/7.76.0-GCCcore-10.3.0 GCC/10.3.0 ncurses/6.2-GCCcore-10.3.0 Python/3.9.5-GCCcore-10.3.0 XZ/5.2.5-GCCcore-10.3.0

Required By

This version of Pysam is a direct dependent of: cgat/0.6.5-foss-2021a CheckM/1.1.3-foss-2021a Megalodon/2.4.2-foss-2021a rmats2sashimiplot/2.0.4-foss-2021a velocyto/0.17.17-foss-2021a

Other Versions

These versions of Pysam are available on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 5th January 2022