Joint Detection of Overlapping Variants

Genotyping can benefit if variants at multiple loci in a single active region are detecting jointly. Joint Detection feature groups loci in a Joint Detection region if the following conditions are met:

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Loci have alleles that overlap each other.

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Loci are in the STR region or less than 10 bases apart of the STR region.

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Loci are less than 10 bases apart of each other.

Joint Detection alters the variant caller algorithm in the part of localized haplotype assembly and genotyping. It generates a haplotype list where all possible combinations of the alleles in the Joint Detection regions are represented. This leads to larger number of haplotypes. During genotyping, Joint Detection calculates likelihoods that each haplotype pair is the truth, given the read pileup is observed. Genotypes likelihoods are calculated as sum of the likelihoods of haplotype pairs that support the alleles in the genotypes. Genotypes with maximum likelihood are reported.

You can enable Joint Detection by setting the --vc-enable-joint-detection option to true. Run time slightly increases when Joint Detection feature is enabled.