ANGSD

Latest version is 0.539 from June 30 2013.

There is also a new version 0.556 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. The program compiles on osx, but this is not tested intensively.

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. All 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 can handle thousands of samples.

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.

Overview of input and intermediary data

The input and intermediary data structures of angsd.

<classdiagram type="dir:LR"> [sequence data]->[genotype;likelihoods] [genotype;likelihoods]->[genotype;probabilities] [sequence files|bam files;SOAP files{bg:orange}]->[sequence data] [glf files|glfv3;soapSNP{bg:orange}]->[genotype;likelihoods] [genotype prob|beagle output{bg:orange}]->[genotype;probabilities] </classdiagram>

Analysis from sequencing data

<classdiagram> // [input|bam files;SOAP files{bg:orange}]->[sequence data]

[sequence data]->[output|summary stats;phat estimates;error estimates{bg:blue}]
</classdiagram>

Analysis from genotype likelihoods

<classdiagram> //[input data|glf files{bg:orange}]->[genotype;likelihoods] [genotype;likelihoods]->[output|glf files;beagle files;MAF estimates;MAF associations;SNP Calling;realSFS;error estimates;Inbreeding{bg:blue}]

</classdiagram>

Analysis from genotype probabilities

<classdiagram> //[input data|beagle output{bg:orange}]->[genotype;probabilities] [genotype;probabilities]->[output|genotype calling;MAF estimates;associations{bg:blue}]

</classdiagram>

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