See http://htslib.org/ for the new 1.0 release of SAMtools, BCFtools, and HTSlib. This website contains information pertaining to the old 0.1.19 samtools release, and so is useful but somewhat out of date. As time permits, this information will be updated for the new samtools/bcftools versions and moved to the new website.


Introduction

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMtools is hosted by SourceForge.net. The project page is here. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:


Publication