Angsd
Description
ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.
License
Free for users.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of angsd and load default version of angsd as
module avail angsd/ # list available modules module load angsd # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail angsd
and choose explicit version you want to use. You can load the module via the command
Documentation
http://www.popgen.dk/angsd/index.php/Quick_Start or angsd --help