altAFplotter: a web app for reliable UPD detection in NGS diagnostics
The detection of uniparental disomies (the inheritance of both chromosome homologues from a single parent, UPDs) is not part of most standard or commercial NGS-pipelines in human genetics and thus a common gap in NGS diagnostics. To address this we developed a tool for UPD-detection based on panel, exome or whole genome sequencing data which is easy to use and publicly available. Detection of UPDs and delineation of different UPD types is achieved by combining two approaches: detection of runs of homozygosity and their extent per chromosome and investigation of variant inheritance and the ratios of uniparentally inherited variants per chromosome. Both metrics have been carefully tuned with a large set of positive and negative controls to allow reliable and sensitive detection of UPDs. We provide a web tool that can be easily accessed and used to enable geneticists to perform a sensitive UPD-detection analysis based on exome, panel and whole genome sequencing data (.vcf-files) on the fly.