Metadata-Version: 1.1
Name: varapp-backend-py
Version: 1.0.1.2
Summary: Genomic variants explorer
Home-page: https://github.com/varapp/varapp-backend-py
Author: Vital-IT/SIB/CHUV
Author-email: julien.delafontaine@sib.swiss
License: GPL-3
Download-URL: https://github.com/varapp/varapp-backend-py/tarball/1.0.1.2
Description: What is Varapp ?
        ----------------
        
        Varapp is an application to filter genetic variants, with a reactive graphical user interface.
        
        The application has been developed in a collaboration between the
        Swiss Institute of Bioinformatics (SIB) and the Lausanne University hospital (CHUV).
        
        The complete documentation is available at
        `https://varapp-demo.vital-it.ch/docs/ <https://varapp-demo.vital-it.ch/docs/>`_ .
        
        .. figure:: /resources/img/main-border.png
           :width:  100%
           :alt: [Main window]
        
        Motivation
        ..........
        
        Common filtering pipelines can be very tedious, including an annotation step,
        complicated forms, multiple exports to spreadsheets, merging and manual curation
        of theses spreadsheets.
        Although there already exist several tools to facilitate the annotation of lists of variants
        and apply basic filters such as frequency in a population, quality or location,
        Varapp has at least one of the following advantages over existing software:
        
        *   **Security**: It does not require to upload data to a cloud or external client;
            one can deploy the app on any local computer and keep the data private.
        
        *   **Fast, non-trivial filtering** based on family pedigree, including complex cases
            such as compound heterozygous, in less than a second for 500K variants.
        
        *   **Reproducibility**: It uses a relational database, adding the potential to cross information
            between experiments, reuse the results of previously studied data,
            and keep track of the annotation/versions used to produce the results.
        
        *   **Reactive user interface**: apply a filter and see the result immediately.
        
        Use cases
        .........
        
        Varapp is typically well-suited to cover the following two use cases,
        the result of which is obtained within a few seconds:
        
        *   **Mendelian diseases**
        
            We consider all variants in the exomes of one or several families
            affected by the same hereditary disease. We are searching for the variants
            that are susceptible to cause the disease.
        
            Varapp provides one-click filters for dominant, recessive, de novo, X-linked,
            and compound heterozygous cases.
        
        *   **Gene panels**
        
            We consider the same few genes (typically a few hundred) 
            in a large series of independent individuals. We seek rare variants with
            strong impact, then inspect the individual(s) that carry them.
        
        What Varapp is not
        ..................
        
        *   ... a variants caller:
        
            It starts after the variant calling has already been done, 
            and works based on the VCF file that the latter produces.
        
        *   ... adapted to full genome sequencing or million genomes projects:
        
            For the moment, the app is responsive with datasets up to 500'000 variants
            and a few hundred individuals,
            but performance issues are expected when dealing with millions of variants,
            as in the case of full genome sequencing, or with thousands of samples.
        
        
        How can I try it?
        -----------------
        
        One demo version of the program is available at `https://varapp-demo.vital-it.ch <https://varapp-demo.vital-it.ch>`_ .
        Log in as user "test" with password "test".
        You will be granted access to a variants database "demo".
        
        Try the following standard filters:
        
        - Recessive scenario
        - 1% frequencies in 1000 Genomes, ESP and EXAC
        - Quality filter: PASS (VQSR)
        - HIGH/MED impact
        
        You should retreive a single variant on gene TBC1D7 that has been published
        in `Hum Mutat. 2014 Apr;35(4):447-51 <http://www.ncbi.nlm.nih.gov/pubmed/24515783>`_.
        
        .. note::
        
            Prior to making it public, this dataset has been anonymized and obfuscated.
            Parents variant data was generated by random shuffling variants from several
            independent exome datasets. Children variant data was derived from the
            shuffled parents data. The TBC1D7 pathogenic variant was then added
            following recessive pattern of inheritance.
        
        .. note::
        
            This version runs on minimal hardware, thus its performance is not comparable
            to a real production setup.
        
        If you liked it, we encourage you to deploy an instance at your own lab
        and share the experience.
        
        
        Contact
        -------
        
        App main developer: `Julien Delafontaine <julien.delafontaine@sib.swiss>`_
Keywords: variants,filter,genotype,gemini
Platform: UNKNOWN
Classifier: Environment :: Web Environment
Classifier: Framework :: Django
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Internet :: WWW/HTTP
Classifier: Topic :: Internet :: WWW/HTTP :: Dynamic Content
