WhatsHap: fast and accurate read-based phasing

Abstract Read-based phasing allows to reconstruct the haplotypes of a sample purely from sequencing reads. While phasing is an important step for answering questions about population genetics, compound heterozygosity, and to aid in clinical decision making, there has been a lack of accurate, usable and standards-based software. WhatsHap is a production-ready tool for highly accurate read-based phasing. It was designed from the beginning to leverage third-generation sequencing technologies, whose long reads can span many variants and are therefore ideal for phasing. WhatsHap works also well with second-generation data, is easy to use and will phase not only SNVs, but also indels and other variants. It is unique in its ability to combine read-based with pedigree-based phasing, allowing to further improve accuracy if multiple related samples are provided.