WhatsHap: fast and accurate read-based phasing

Correspondence: [email protected] Center for Bioinformatics, Saarland University, Campus E2.1, 66123, Saarbrücken, Germany Max Planck Institute for Informatics, Saarbrücken, Germany Full list of author information is available at the end of the article †Equal contributor Abstract Read-based phasing allows to reconstruct the haplotype structure of a sample purely from sequencing reads. While phasing is a required step for answering questions about population genetics, compound heterozygosity, and to aid in clinical decision making, there has been a lack of an 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 genetic phasing, allowing to further improve accuracy if multiple related samples are provided.