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How do we filter positions on the X and Y chromosome?

Males are hemizygous for the X and Y chromosome, thus the concept of diploid genotypes does not apply here. However, all common variant callers are currently dealing with these positions as if they were diploid. This means in vcf format a hemizygous variant on a male X chromosome would be reported as if it were a homozygous variant of a diploid genetic background. therefore we apply our diploid genotype vector for frequency filtering also for the X and Y chromosome no matter whether the sample is actually hemizygous or not.

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