WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.


  • Very accurate results (Martin et al., WhatsHap: fast and accurate read-based phasing)

  • Works well with Illumina, PacBio, Oxford Nanopore and other types of reads

  • It phases SNVs, indels and even “complex” variants (such as TCGAGAA)

  • Pedigree phasing mode uses reads from related individuals (such as trios) to improve results and to reduce coverage requirements (Garg et al., Read-Based Phasing of Related Individuals).

  • WhatsHap is easy to install

  • It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs.

  • It produces standard-compliant VCF output by default

  • If desired, get output that is compatible with ReadBackedPhasing

  • Open Source (MIT license)


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