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>

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

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

<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>

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

</classdiagram>

Analysis of Next Generation Sequencing Data

This is a general purpose software for analysis of next generation sequencing data including QC, Association and population genetic analysis.

ANGSD has its own wiki at http://popgen.dk/angsd