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.
Versions freely available to all users:
Free for users.
You can load the module via the command
module add angsd-0.920 angsd --help
This makes available the path to the program binaries, libraries and manual pages.
Documentation is available on http://www.popgen.dk/angsd/index.php/Quick_Start or