View source for SAMtools

== Introduction ==

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.

== Installed Version ==

The currently installed versions are:

 On environment ''hpc-uniol-env''
 SAMtools/0.1.16
 SAMtools/1.3.1
 SAMtools/1.3.1-intel-2016b
 SAMtools/1.7-foss-2016b
 SAMtools/1.8-intel-2016b

 On environment ''hpc-env/6.4'' 
 SAMtools/1.7-foss-2017b
 SAMtools/1.8-intel-2018a
 SAMtools/1.9-foss-2017b

 On environment ''hpc-env/8.3'' 
 SAMtools/1.9-foss-2019b

== Using SAMtools on the HPC cluster ==

If you want to use SAMtools on the HPC cluster, you will have to load its corresponding module first. You can do that with the command
 module load/1.3.1
Since there are multiple version of SAMtools installed, you can specify your needed version by changing the last part of the "module load"-command, e.g.
 module load/0.1.16

would load version '''0.1.16''' instead of version '''1.3.1'''.

== Documentation ==

The full documentation can be found [http://www.htslib.org/doc/ here].