PT  - JOURNAL ARTICLE
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
TI  - WhatsHap: fast and accurate read-based phasing
AID  - 10.1101/085050
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 085050
4099  - http://biorxiv.org/content/early/2016/11/02/085050.short
4100  - http://biorxiv.org/content/early/2016/11/02/085050.full
AB  - 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.