Detecting false positive variant calls in next-generation sequencing

Abstract

A method for detecting false positive variant calls in a next generation sequencing analysis pipeline involves obtaining a plurality of read pileup windows associated with a first sample genome. The method also involves obtaining, for each reference nucleotide position represented in the plurality of read pileup windows, a label indicating that the reference nucleotide position is either (i) a known variant or (ii) a non-variant. The method further involves training a neural network based on data indicative of the plurality of read pileup windows and the labels. Additionally, the method involves receiving a read pileup window associated with a second sample genome. Further, the method involves determining, using the trained neural network, a likelihood that the read pileup window associated with the second sample genome represents a variant.