ANGSD is a software for analyzing next generation sequencing data intended for use with mapped reads to imputed genotype probabilities. ANGSD can work with BAM files but is not meant for manipulating them. SAMTools is best for that. ANGSD is ideal for use with low to medium depth genomic data.
Using ANGSD on HPC Systems
In order to access ANGSD on the HPC system, you will need to load the GNU module as the software is compiled with the GNU 8.3.1 compilers. Once that module is loaded, the angsd command will become available. For example:
module load gnu angsd # --- Typing angsd with nothing after it will print usage information ## An example of a call to ANGSD to compute allele frequencies on a BAM file list angsd -b bam.filelist -GL 1 -doMajorMinor 1 -doMaf 2 -P 5
Additional information on ANGSD can be found on their Home Page. In addition, there is an Quick Start Tutorial page to help get you started with ANGSD. This tutorial page and all of its steps should work on the HPC system.