Skip to content
Public repository for VariantValidator project
Python Other
  1. Python 99.8%
  2. Other 0.2%
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
VariantValidator Merged v1.0.0 into master Aug 12, 2019
bin
configuration Removed liftover location so is always downloaded on first use Jul 29, 2019
docs
tests
.coverage
.gitignore Merged v1.0.0 into master Aug 12, 2019
.travis.yml Updated travis file so it won't fill database twice Jul 17, 2019
Dockerfile Added instructions and Dockerfiles for docker installation Jul 24, 2019
LICENSE.txt add liscense information and update setup.py with some version changes Nov 7, 2018
MANIFEST.in Removed old version file from manifest Jul 9, 2019
README.md Modified docs that helped me install and successfully test vvPy3. Not… Jul 25, 2019
docker-compose.yml Added instructions and Dockerfiles for docker installation Jul 24, 2019
environment.yml Merged v1.0.0 into master Aug 12, 2019
requirements.txt Added biopython to project requirements Jul 29, 2019
requirements_dev.txt Added biopython to project requirements Jul 29, 2019
setup.py Change setup-py to ensure vvhgvs installs Aug 5, 2019
vdb_docker.df Added instructions and Dockerfiles for docker installation Jul 24, 2019

README.md

VariantValidator

codecov Build Status

About

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 inter-converts 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 locally on Mac OS X or Linux-compatible computers. It can also work within a docker container.

Required software:

  • MySQL
  • Python 3.6 or above
  • SQLite version 3.8.0 or above

Optional software:

  • Postgres version 9.5 or above, Postgres 10 is not supported.

For installation instructions please see INSTALLATION.md. For the older python 2 version, see previous releases.

Operation and configuration

Please see MANUAL.md. Note that the latest version is not compatible with previous releases.

License

Please see LICENSE.txt

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) 2019 VariantValidator Contributors

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/.

You can’t perform that action at this time.