Pysam is a python module for reading and manipulating files in the SAM/BAM format. The SAM/BAM format is a way to store efficiently large numbers of alignments (Li 2009), such as those routinely created by next-generation sequencing methods.
Pysam is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
The latest version is available through pypi. To install, simply type:
pip install pysamIf you are using the conda packaging manager (e.g. miniconda or anaconda), you can install pysam from the bioconda channel:
conda config --add channels r
conda config --add channels bioconda
conda install pysam
Pysam documentation is available through https://readthedocs.org/ from here
Questions and comments are very welcome and should be sent to the pysam user group