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 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