Samtools
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
.