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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README.rst

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:

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.

Pysam is available through pypi. To install, type:

pip install pysam

Pysam documentation is available here

Questions and comments are very welcome and should be sent to the pysam user group