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.
Please cite us if you use WhatsHap.
- 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
- 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)
We run a public mailing list. Please don’t hesitate to post questions and comments.
Table of contents¶
- User guide
- Questions and Answers
- Various notes
- How to cite