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We provide tools for polyploid data, covering topics from genotype calling, over linkage mapping to haplotyping. Further, we intend to provide tools to simulate polyploid data sets for given genotypes and population structures.Our methods may be applied to species of any level of ploidy.
The project summary page is already available here.
The is the first version of the project. Requires installation of boost, DAKOTA and a framework to support parallelization call TBB. This package implements the following methods.
Haplotype phasing:
This method takes the genotypes, the physical ordering of SNPs and the ploidy as input and determines
the phased haplotypes for all the samples
This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 289974.