Samtools

Owned by Simon Alexander, created
Last updated: Oct 20, 2022
1 min read
1 Overview | 2 Using

Overview

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.

Using

Use the module name htslib, samtools and bcftools to discover versions available and to load the application.

Multicore:

Both samtools and bcftools can run across multiple threads using the --threads option.

Please see the help for the specific tool’s command for further details e.g. samtools view / bcftools mpileup.