Assessing Allelic Configuration Models in Fixed Ploidy Variant Calling Using R

Genotyping of SNP loci polyploids has always been challenging, but may become easier using high-coverage sequencing. The production of such data in turn requires the development of new methods and software that can be used to analyse it in user friendly software such as the CLC Genomics Workbench. The Fixed Ploidy Variant Detection tool of the CLC Genomics Workbench already takes higher ploidy levels into account, but an explicit evaluation of the locus configuration is currently not provided. We have developed an algorithm that uses read counts and average base quality to estimate the most likely allelic configuration at each variant position in polyploid samples. The underlying model
uses a log-likelihood approach and the applications for this are very broad. Not only population genetics, but also cancer research and haplotype based analyses can benefit from this. We are applying the algorithm to a Betula RAD data set to investigate introgression and gene flow in three species of the genus. Independently, a read-based haplotype caller is currently being developed at CLC bio. The number of called haplotypes and their support is expected to correlate with the locus configuration and will serve as a validation of our approach.