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pysam: htslib interface for python

Author: Andreas Heger, Kevin Jacobs and contributors
Date: |today|
Version: |version|

Pysam is a python module for reading, manipulating and writing genomic data sets.

Pysam is a wrapper of the htslib_ C-API and 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. The module supports compression and random access through indexing.

This module provides a low-level wrapper around the htslib_ C-API as using cython and a high-level, pythonic API for convenient access to the data within genomic file formats.

The current version wraps htslib-1.7, samtools-1.7 and bcftools-1.6.

To install the latest release, type:

pip install pysam

See the :ref:`Installation notes <installation>` for details.

Contents

.. toctree::
   :maxdepth: 2

   api.rst
   usage.rst
   installation.rst
   faq.rst
   developer.rst
   release.rst
   benchmarking.rst
   glossary.rst

Indices and tables

Contents:

References

[Li2009]The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8. PMID: 19505943
.. seealso::

   Information about htslib
      http://www.htslib.org

   The samtools homepage
      http://samtools.sourceforge.net

   The cython C-extensions for python
      http://cython.org/

   The python language
      http://www.python.org