phase genomic variants using DNA sequencing reads
Project description
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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.
:target: https://pypi.python.org/pypi/whatshap
.. image:: https://semaphoreci.com/api/v1/whatshap/whatshap/branches/master/shields_badge.svg
:target: https://semaphoreci.com/whatshap/whatshap
.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
:target: http://bioconda.github.io/recipes/whatshap/README.html
|
.. image:: https://bitbucket.org/repo/8AjxBd/images/543323972-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.
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.
Project details
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