Samtools

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

Description

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

• Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
• BCFtools: Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
• HTSlib: A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Note: This page does not cover all features of SAMtools. Please refer to Samtools for the complete list of all subtools.

Availability and Loading Module

To query all available version of SAMtools in our clusters:

[name@server ~]$ module spider samtools

You can load the version of your choice using module load. For example, to load samtools 1.12 use command

[name@server ~]$ module load samtools/1.12

To load the default version of samtools use command

[name@server ~]$ module load samtools

[name@server ~]$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.12 (using htslib 1.12)

Usage:   samtools <command> [options]