===== Pysam

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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_.

If you are using the conda packaging manager (e.g. miniconda or anaconda), you can install pysam from the bioconda channel <https://bioconda.github.io/>_::

conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict conda install pysam

Installation through bioconda is the recommended way to install pysam as it resolves non-python dependencies and uses pre-configured compilation options. Especially for OS X this will potentially save a lot of trouble.

The current version of pysam wraps 3rd-party code from htslib-1.23.1, samtools-1.23.1, and bcftools-1.23.1.

Pysam is available through PyPI <https://pypi.org/project/pysam/>_. To install, type::

pip install pysam

Pysam documentation is available here <http://pysam.readthedocs.org/en/latest/>_

Questions and comments are very welcome and should be sent to the pysam user group <http://groups.google.com/group/pysam-user-group>_

.. _samtools: http://samtools.sourceforge.net/ .. _tabix: http://samtools.sourceforge.net/tabix.shtml .. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943

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