pysam: htslib interface for python

Author:Andreas Heger, Kevin Jacobs and contributors
Date:Jun 18, 2017

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-1.3, samtools-1.3 and bcftools-1.3.

To install the latest release, type:

pip install pysam

See the Installation notes for details.


Indices and tables



[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

See also

Information about htslib
The samtools homepage
The cython C-extensions for python
The python language