Angsd

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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

Homepage

http://www.popgen.dk/angsd/index.php/ANGSD