Fig. 1

Overview of a typical alignment-free genotyping approach. First, kmers covering each allele of each variant is stored (step 1), e.g. by choosing kmers from a graph representation of the variants. All kmers from the reads are then collected (step 2), and genotype probabilities are computed using Bayes rule with genotype probabilities from a known population used as priors (step 3). The most likely genotype is chosen