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pysam: htslib interface for python

Author

Andreas Heger, John Marshall, Kevin Jacobs, and contributors

Date
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-1.18, samtools-1.18, and bcftools-1.18.

To install the latest release, type:

pip install pysam

See the Installation notes <installation> for details.

This module is unrelated to NREL-PySAM, which wraps the National Renewable Energy Laboratory's System Advisor Model.

Contents

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

Indices and tables

Contents:

  • genindex
  • modindex
  • search

References

Information about htslib

http://www.htslib.org

The samtools homepage

http://samtools.sourceforge.net

The cython C-extensions for python

https://cython.org/

The python language

https://www.python.org

Bonfield.2021

HTSlib: C library for reading/writing high-throughput sequencing data. Bonfield JK, Marshall J, Danecek P, Li H, Ohan V, Whitwham A, Keane T, Davies RM. GigaScience (2021) 10(2) giab007. PMID: 33594436.

Danecek.2021

Twelve years of SAMtools and BCFtools. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. GigaScience (2021) 10(2) giab008. PMID: 33590861.

Li.2009

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 btp352. PMID: 19505943.