We are happy to announce WhatsHap, a tool that phases variants with the help of sequencing reads. It was designed to fully exploit PacBio and Oxford Nanopore reads, which are well-suited for phasing because they span many variants. WhatsHap works also well on Illumina data. WhatsHap gives highly accurate results according to our comparison.
WhatsHap expects a VCF and a BAM file as input, and it outputs a standards-compliant VCF file with added phasing information.
WhatsHap can even make use of related samples such as trios by combining read-based phasing with genetic phasing, boosting the accuracy even further.
- Open Source (MIT license)
- Phases insertions and deletions
- Installable from PyPI or bioconda
- Can use reads from multiple technologies (such as PacBio and Illumina) simultaneously
- Optionally outputs ReadBackedPhasing-compatible VCFs
- Accepts already phased VCFs as input, letting you combine 10X Genomics output with PacBio, for example
- Comes with extra subcommands for working with phased VCFs
- Helps you in visualizing phasing results
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