Customized de novo mutation detection for any variant calling pipeline: SynthDNM

MotivationAs sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines. ResultsHere, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling. AvailabilitySynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm) Contactjsebat@ucsd.edu Supplementary informationSupplementary data are available at Bioinformatics online.