Overview
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. The software is written in C++ and has been used on large sample sizes. This program is not for manipulating
BAM/CRAM files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfile
Using
Use the module name angsd to discover versions available and to load the application.
Multicore
The angsd application allows you define multiple cores/threads within the calls using the '-nThreads or -P for number of threads allocated to the program' options. See angsd --help for more information.