whatshap 2.0

phase genomic variants using DNA sequencing reads

WhatsHap

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.

Features

• 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 TCG → AGAA)

• 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)

Documentation

• GitHub repository

• Read the documentation online. Offline documentation is available in the doc/ subdirectory in the repository and in the downloaded tar distribution.

Issue tracker

Please do not hesitate to use our issue tracker for bug reports and feature requests.