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VariantValidator Merged v1.0.0 into master Aug 12, 2019
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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 for details of the hgvs package

VariantValidator is a highly functional platform enabling high-throughput and embeddable utilisation of functionality of


The basic functionality of and VarinantValidator is documented here

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


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 For the older python 2 version, see previous releases.

Operation and configuration

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


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

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