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phase genomic variants using DNA sequencing reads

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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.

Please :ref:`cite us if you use WhatsHap <howtocite>`.


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 :ref:`easy to install <installation>`
* It is :ref:`easy to use <user-guide>`: 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
-------------

* `Bitbucket page <https://bitbucket.org/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.


Mailing list
------------
We run a `public mailing list <https://lists.cwi.nl/mailman/listinfo/whatshap>`_. Please
don't hesitate to post questions and comments.

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