ANGSD

Latest version is 0.539 from June 30 2013.

There is also a new version 0.572 which has passed our internal tests, but use at own risk. This versions gives results similar to older versions, but some minor options might be renamed, and the output files could be compressed. For some methods, you might not want to dump intermediate results, then some ('not all') output can be disabled by adding a '-' minus infront of the argument.

The program is developed on tested on a Linux system.

There is a (very) short tutorial.

About

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.

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 2 -doMajorMinor 1 -nThreads 10