Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts
Miklós Dióssy, Zsófia Sztupinszki, Marcin Krzystanek, Judit Börcsök, Aron C. Eklund, István Csabai, Anders Gorm Pedersen, Zoltán Szállási
Abstract
Formalin-fixed paraffin-embedded tissue, the most common tissue specimen stored in clinical practice, presents challenges in the analysis due to formalin-induced artifacts. Here, we present Strand Orientation Bias Detector (SOBDetector), a flexible computational platform compatible with all the common somatic SNV-calling pipelines, designed to assess the probability whether a given detected mutation is an artifact. The underlying predictor mechanism is based on the posterior distribution of a Bayesian logistic regression model trained on The Cancer Genome Atlas whole exomes. SOBDetector is a freely available cross-platform program, implemented in Java 1.8.