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Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

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|build-status| |docs|

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 

conda config --add channels defaults conda config --add channels conda-forge conda config --add channels bioconda 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-1.14, samtools-1.14, and bcftools-1.14.

Pysam is available through

_. To install, type::

pip install pysam

Pysam documentation is available


Questions and comments are very welcome and should be sent to the

pysam user group 

.. _samtools: .. _tabix: .. _Li 2009:

.. |build-status| image:: :alt: build status :scale: 100% :target:

.. |docs| image:: :alt: Documentation Status :scale: 100% :target:

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