whatshap

.. image:: https://img.shields.io/pypi/v/whatshap.svg?branch=main :target: https://pypi.python.org/pypi/whatshap

.. image:: https://github.com/whatshap/whatshap/workflows/CI/badge.svg

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg :target: http://bioconda.github.io/recipes/whatshap/README.html

|

.. image:: https://github.com/whatshap/whatshap/raw/main/logo/whatshap_logo.png

|

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 <https://doi.org/10.1101/085050>_)
• 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 <https://doi.org/10.1093/bioinformatics/btw276>_).
• 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 <https://github.com/whatshap/whatshap/>_
• Read the documentation online <https://whatshap.readthedocs.io/>_. 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 <https://github.com/whatshap/whatshap/issues>_ for bug reports and feature requests.