SYSTEMS AND METHODS FOR CALLING VARIANTS USING METHYLATION SEQUENCING DATA

摘要

An allelic position variant calling method using a prior genotype probability at the allelic position is provided. A strand specific base count set in forward and reverse directions for the allelic position is obtained, using strand orientation and identity of a respective base at the allelic position in each respective nucleic acid fragment sequence that maps to the allelic position, where bases at the allelic position whose identity can be affected by conversion of cytosine to uracil do not contribute to the strand specific base count set. Respective forward and reverse strand conditional probabilities are computed for each candidate genotype for the allelic position using the strand specific base count set and sequencing error estimate. Likelihoods are computed using a combination of these conditional probabilities and the prior genotype probability. From this, a determination is made as to whether the likelihoods support a variant call at the allelic position.