TY - JOUR T1 - WhatsHap: fast and accurate read-based phasing JF - bioRxiv DO - 10.1101/085050 SP - 085050 AU - Marcel Martin AU - Murray Patterson AU - Shilpa Garg AU - Sarah Fischer AU - Nadia Pisanti AU - Gunnar W Klau AU - Alexander Schöenhuth AU - Tobias Marschall Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/02/085050.abstract N2 - 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. ER -