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README.txt
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# About VariantFormatter
VariantValidator is a software tool designed to accept genomic level sequence variant
descriptions in the pseudo-VCF or HGVS formats (see MANUAL.md), and automatically generate
relevant transcript-level and protein-level HGVS variant descriptions.
VariantFormatter interfaces with a custom version of the hgvs package to parse, format,
and manipulate biological sequence variants.
See https://github.com/biocommons/hgvs/ for details of the hgvs package
See https://github.com/openvar/vv_hgvs for the custom version of the hgvs package
## Features
The basic functionality of VariantFormatter is documentes in the MANUAL.md
VariantFormatter simultaneously and accurately projects genomic sequence variations onto
all overlapping transcript reference sequences
VariantFormatter can be used as a variant-by-variant processor or as a batch processor
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
## Web-API
http://rest.variantvalidator.org
## Pre-requisites
VariantFormatter will work on Mac OS X or Linux-compatiable computers.
Required software:
* MySQL
* Python 2.7
Optional software:
* Postgres version 9.5 or above
* SQLite version 3.8.0 or above
For installation instructions please see [INSTALLATION.md](INSTALLATION.md)
# Operation and configuration
Please see [MANUAL.md](MANUAL.md)
## License
Please see [LICENSE.txt](LICENSE.txt)
## Cite us
VariantFormatter is a sub-project of the VariantValidator project
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 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/>.
> </LICENSE>
> <LICENSE>
> Copyright (C) 2019 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/>.
> </LICENSE>