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rest_VariantValidator

Build Status codecov

About rest_variantValidator

rest_variantValidator is a rest web interface for VariantValidator

About VariantValidator

VariantValidator is a user-friendly software tool designed to validate the syntax and parameters of DNA variant descriptions according to the HGVS Sequence Variant Nomenclature.

VariantValidator ensures that users are guided through the intricacies of the HGVS nomenclature, e.g. if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator accurately interconverts between transcript variant descriptions and genomic variant descriptions in HGVS and Variant Call Format (VCF)

VariantValidator interfaces with the hgvs package to parse, format, and manipulate biological sequence variants. See https://github.com/biocommons/hgvs/ for details of the hgvs package

VariantValidator is a highly functional platform enabling high-throughput and embeddable utilisation of functionality of https://variantvalidator.org/

Features

The basic functionality of https://variantvalidator.org/ and VarinantValidator is documented here https://www.ncbi.nlm.nih.gov/pubmed/28967166

VariantValidator simultaneously and accurately projects genomic sequence variations onto all overlapping transcript reference sequences, and vice-versa

Alternatively, genomic sequence variation can be projected onto a specified single, or specified subset of transcript reference sequences for any given gene

Projection of sequence variations between reference sequences takes account of discrepancies between genomic and transcript reference sequences, thus ensuring an accurate prediction of the effect on encoded proteins for every gene

For sequence variations falling within the open reading frames of genes, VariantValidator automatically projects sequence variants via the transcript reference sequence onto genome builds GRCh38, GRCh37, hg38 and hg19 (HGVS format and VCF components), including projection onto relevant Alternative genomic reference sequences, the composition of which varies between patched GRC genome builds and static hg genome builds

Pre-requisites

VariantValidator will work on Mac OS X or Linux operating systems.

Required software:

  • MySQL
  • Python 2.7
  • SQLite version 3.8.0 or above

Optional software:

  • Postgres version 9.5 or above

For installation instructions please see INSTALLATION.md

Operation and configuration

Please see MANUAL.md

Running in docker

Please see DOCKER.md

License

Please see LICENSE.txt

Terms and conditions of use

Terms and conditions can be found here

Cite us

Hum Mutat. 2017 Oct 1. doi: 10.1002/humu.23348

VariantValidator: Accurate validation, mapping and formatting of sequence variation descriptions.

Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.

Copyright (C) 2018 Peter Causey-Freeman, University of Leicester

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.