Multiallelic Genotyping Of Single Nucleotide Polymorphisms And Indels

A method for genotyping one or more multiallelic markers using a computer system, the method comprising:

• acquiring signals for one or more multiallelic markers in one or more samples;
• for each multiallelic marker, clustering the signals for each pair of alleles in a plurality of allele pairs from the one or more samples, resulting in clusters representing each allele pair;
• for each homozygous cluster representing a homozygous allele pair, collecting signals for an alternative allele for calculation of a background signal for the alternative allele, resulting in a plurality of background signals each representing a respective allele;
• assigning initial genotype calls for each sample for each allele pair based upon the signals and the background signals;
• calculating a multivariate normal distribution for each cluster using the initial genotype calls and prior cluster parameters;
• for each multivariate normal distribution for each cluster, calculating a logarithmic likelihood of membership for each sample;
• based on the logarithmic likelihood of membership, calculating, for each sample, a probability of membership in each cluster;
• and
• assigning a final genotype call to each sample based on the probability of membership.