Difference between revisions of "SAMtools"
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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 | 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 | module load/1.3.1 | ||
Since there are multiple version of SAMtools installed, you can specify your | 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 | module load/0.1.16 | ||
would load version '''0.1.16''' instead of version '''1.3.1'''. | |||
== Documentation == | == Documentation == | ||
The full documentation can be found [http://www.htslib.org/doc/ here]. | The full documentation can be found [http://www.htslib.org/doc/ here]. | ||
Revision as of 09:08, 15 May 2017
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 version is 0.1.16 and 1.3.1.
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 here.
