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[edit | edit source]
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[edit | edit source]
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[edit | edit source]
SAMtools, BCFtools, and HTSlib are typically used on the command line. They are also used as libraries for other programs to use.
See also[edit | edit source]
References[edit | edit source]
| SAMtools Resources | |
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Contributors: Prab R. Tumpati, MD
