Unfazed: parent-of-origin detection for large and small de novo variants

Abstract

Abstract Summary Unfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30 000 de novo variants in under 60 h. Availability and implementation Unfazed is available at https://github.com/jbelyeu/unfazed. Supplementary information Supplementary data are available at Bioinformatics online.