a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages.
Pysam is installed as a module within python.
InstallationUse the following command to install this title with the CLI client:
$ sbgrid-cli install pysam
Citation NoteUsers of the program should cite the url https://github.com/pysam-developers/pysam
Andreas Heger, Kevin Jacobs