pysam: samtools interface for python

Author:Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Leo Goodstad, Kevin Jacobs Date:February 14, 2011 Version:0.4.1

The SAM/BAM format is a way to store efficiently large numbers of alignments [Li2009], such as those routinely are created by next-generation sequencing methods.

This module provides a low-level wrapper around the samtools C-API using cython and a high-level API for convenient access to the data in SAM/BAM formatted files. Also included is an interface to the tabix C-API for reading compressed and indexed tabular data.

The current version wraps samtools-0.1.12a and tabix-0.2.3.

Contents

• pysam - An interface for reading and writing SAM files
  • API
• Usage
  • Opening a sampfile
  • Fetching mapped reads in a region
  • Using the pileup-engine
  • Using samtools commands within python
  • Creating SAM/BAM files from scratch
  • Using streams
  • Using the samtools SNP caller
• Glossary
• Developer’s guide
  • Code organization
  • Importing csamtools
  • Unit testing
• Release notes
  • Release 0.4.1
  • Release 0.4
  • Release 0.3

Indices and tables

Contents:

• Index
• Module Index
• Search Page

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

See also

The samtools homepage

http://samtools.sourceforge.net

The cython C-extensions for python

http://cython.org/

The python language

http://www.python.org