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 0.16.0.1-GCC-9.3.0
To load the module for Pysam 0.16.0.1-GCC-9.3.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load Pysam/0.16.0.1-GCC-9.3.0
BEAR Apps Version
For more information visit the Pysam website.
This version of Pysam has a direct dependency on: cURL/7.69.1-GCCcore-9.3.0 GCC/9.3.0 ncurses/6.2-GCCcore-9.3.0 Python/2.7.18-GCCcore-9.3.0 Python/3.8.2-GCCcore-9.3.0 XZ/5.2.5-GCCcore-9.3.0
This version of Pysam is compatible with multiple vesions of Python. At any time, only one of the versions of Python can be active and the desired version of Python should be loaded before loading this version of Pysam.
This version of Pysam is a direct dependent of: CNVkit/0.9.8-foss-2020a-Python-3.8.2-R-4.0.0 deepTools/3.5.0-foss-2020a-Python-3.8.2 HTSeq/0.13.5-foss-2020a-Python-3.8.2
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 3rd December 2020