Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate bundles:
- Samtools is for reading/writing/editing/indexing/viewing SAM/BAM/CRAM format.[1]
- BCFtools is for reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants[2]
- HTSlib is a C library for reading/writing high-throughput sequencing data.[3] It is installed as part of SAMtools.
Picotte
Installed Version
HTSlib + BCFtools + Samtools 1.12 is installed. Use the modulefile:
samtools/1.12
Loading a samtools module will automatically load the appropriate bcftools and htslib modules. (Plus other modules, e.g. Perl.)
You can also load HTSlib and BCFtools separately:
htslib/1.12
bcftools/1.12
Proteus
Installed Versions
Multiple versions of Samtools + BCFtools + HTSlib are installed. Pick one:
samtools/1.2
samtools/1.3.1
samtools/1.8
samtools/1.10
Loading a samtools module will automatically load the appropriate bcftools and htslib modules. (Plus other modules, e.g. Perl.)
References
[2]
[3]