View source for 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 [http://samtools.sourceforge.net/ 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. This of course requires that users also install htslib.

<!-- ** 
==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;SFS{bg:blue}]
 </classdiagram>
-->

=Synopsis=
<code lang=sh>
./angsd [OPTIONS]
</code>

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

<code lang=sh>
./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 1 -doMajorMinor 1 -nThreads 10
</code>

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.