Methylation-based false positive duplicate marking reduction

Abstract

An analytics system marks duplicate fragments from an initial set of fragments from a subject. The analytics system generates a sample state vector for each fragment. Each sample state vector comprises a sample genomic location within a reference genome and a plurality of methylation states for a plurality of CpG sites in the fragment, the methylation states determined to be one of methylated, unmethylated, variant, and ambiguous. The analytics system identifies two fragments with methylation state vectors as being derived from a matching reference location, e.g., sharing a common plurality of CpG sites. The analytics system calculates a modified Hamming distance based on methylation states in the first sample state vector and methylation states in the second sample state vector. Based on the modified Hamming distance, the analytics system marks the first fragment and the second fragment as either duplicate fragments or non-duplicate fragments.