There is a newer version of PysamPysam 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 0.18.0-GCC-11.2.0
To load the module for Pysam 0.18.0-GCC-11.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load Pysam/0.18.0-GCC-11.2.0
BEAR Apps Version
For more information visit the Pysam website.
This version of Pysam has a direct dependency on: cURL/7.78.0-GCCcore-11.2.0 GCC/11.2.0 ncurses/6.2-GCCcore-11.2.0 Python/3.9.6-GCCcore-11.2.0 XZ/5.2.5-GCCcore-11.2.0
This version of Pysam is a direct dependent of: CIRI-long/1.1.0-foss-2021b CMSeq/1.0.4-foss-2021b MetaPhlAn/3.0.14-foss-2021b methylartist/1.2.6-foss-2021b nanopolish/0.14.0-foss-2021b SplAdder/3.0.3-foss-2021b
These versions of Pysam 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 14th July 2022