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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 project is still under development. A first version will be released soon.This package implements the following methods.
Genotype calling:
This method takes the raw signals of SNPs as input, determines the ploidy of the species and performs the genotype calling on all the samples.
Linkage mapping:
This method takes the genotypes as input, estimates the recombination frequencies and determines the physical order of the marker SNPs.
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.