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I had a few questions about the haplotype score.
In the technical documentation it states that "Higher scores are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls. Note that the Haplotype Score is only calculated for sites with read coverage."
How is the haplotype group for each variant site determined? e.g. Does it take the closest two variants to the query site and then treat the query variant + closest two variants as the haplotype group?
Also, in the case of multiallelic SNPs (>2 SNPs), haplotype score is inappropriate since it only looks at whether a site can be explained by the segregation of two and only two haplotypes, correct? So multiallelic snps will be assigned poor haplotype scores OR will these sites not be annotated at all? If we have a case where there is a truly biallelic SNP and a couple of samples have some reads that are erroneously calling a third allele, this variant site will be assigned a poor haplotype score overall, correct?