ANGSD

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' files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying bamfiles.

ANGSD is also on github now: https://github.com/ANGSD/angsd

We recognize that CRAM is an emerging format for storing NGS data. We have therefore begun including CRAM support by using the htslib in the latest github version --branch=withhtslib. This of course requires that users also install htslib.

Synopsis

./angsd [OPTIONS]

example of allele frequency estimated from genotype likelihoods with bam files as input using 10 threads

./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 1 -doMajorMinor 1 -nThreads 10

There is a (very) short Quick Start, which contains a test data set you can download, and will contain some useful examples.

Platform

The program is developed on tested on a Linux system with gcc compiler. It compiles on OSX with clang, but OSX is not really that tested.