SAMtools

SAMtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

• SAMtools: Reading, writing, and editing SAM (Sequence Alignment/Map) format files, and calling variants from them.
• BCFtools: Reading, writing, and editing BCF2 (Binary Call Format) files, and calling variants from them.
• HTSlib: A C library for reading and writing high-throughput sequencing data.

Overview

SAMtools, BCFtools, and HTSlib are used to manipulate high-throughput sequencing data. They can handle data in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map), and CRAM formats, and VCF (Variant Call Format) and BCF (Binary Call Format) variant calling formats.

Features

SAMtools has various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing, and generating alignments in a per-position format. BCFtools also has several utilities for variant calling and manipulating VCFs and BCFs.

Usage

SAMtools, BCFtools, and HTSlib are typically used on the command line. They are also used as libraries for other programs to use.

See also

• Sequence Alignment/Map
• Binary Alignment/Map
• Variant Call Format
• Binary Call Format

References

SAMtools Resources
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