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.
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
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-1.11, samtools-1.11, and bcftools-1.11.
Pysam is available through
pypi_. 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: 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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