Samtools¶
Samtools can be used to manipulate NGS data. The bundle packages version 1.22.1.
Usage example¶
The following command can be executed in the terminal to load the bundle:
The module makes the following commands available:
The samtools_shell command can be used to access a shell in the bundle.
Run pet list -t samtools for a list of examples. The examples were taken from
Wayne University.
Performance notes¶
No performance notes available
Recommended resources per session¶
Samtools should be run on a system with at least 64 GB of RAM and 8 threads.
Benchmarks¶
No benchmarks available.
Community guides and tutorials¶
- No community guides available.
Official site and documentation¶
Licensing information¶
Samtools is licensed under the MIT/Expat license.
Primary citation¶
Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, doi
External guides and resources¶
- If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za