Allele calling/genotyping approaches using k-mers for repetitive polymorphic loci.
Each approach outputs a list of alleles/genotypes and the probabilistic scores for each, where the largest score indiciates the called allele/genotype.
Generate k-mer count proifles for each known allele and compare to k-mer count profile from a set of sequencing reads with unknown genotype.
Get outermost k-mer pairs for each read pair in a set of sequencing reads with unknown genotype and locate the k-mer pairs in known alleles. Using the expected average fragment length for the reads, determine similarity to distance between k-mer pairs in known alleles.
Get information about k-mer count profiles for a list of known alleles. Print out the count profiles for each allele, determine which alleles share count profiles, or determine per-k-mer count differences between pairs of alleles.
Get a list of all possible diploid genotypes given a list of known alleles.