ANGSD: Difference between revisions
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Analysis of Next Generation Sequencing Data | = 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 has its own wiki at http://popgen.dk/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> | |||
Latest revision as of 10:19, 25 June 2013
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
<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>