The Fixed Ploidy Variant Caller

The purpose of the Fixed Ploidy Variant Caller is to call variants in samples with known ploidy from read mapping data. It can detect variants in samples from haploid (e.g. bacteria), diploid (e.g. human) and polyploid (upto tetraploid) organisms (e.g. higher plants). It detects Single Nucleotide Variants (SNVs), MNVs (Multiple Nucleotide Variants), insertions, deletions as well as replacements (combinations of neighboring insertions, deletions and SNVs for which the positions are ambiguous).

The algorithm behind the Fixed Ploidy Variant Caller combines a Bayesian model with a Maximum Likelihood approach. Variants are called by examining the posterior probabilities from the Bayesian model: at any given site a variant is called if the sum of the posterior probabilities of the site types that are different from the homozygous reference allele site type is larger than the user-specified 'probability' cut-off value. The variant called is the variant that corresponds to the site type with the highest posterior probability. When evaluating the posterior probabilities in the Bayesian model, maximum likelihood estimates for the parameters of the model are used. These are obtained from the likelihood function using an Expectation Maximization (EM) approach.