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WhatsHap: fast and accurate read-based phasing

By Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O. Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schöenhuth, Tobias Marschall

Posted 02 Nov 2016
bioRxiv DOI: 10.1101/085050

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.

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