SNP Annotation Tool

SNPnexus COVID is a cutting-edge analytical platform that allows researchers to analyse the functional implication of variants in COVID-19 patient genomes and to prioritise these variants based on sequences that demonstrate clinical utility for the prevention, management and/or treatment of COVID-19. It can also provide unique insights into variations in the pathogenesis of COVID-19 patient cohorts among distinct populations.
SNPnexus if freely available for academic and non-profit use only.
If you are a commercial user/service provider, or if you are interested in a customised version of SNPnexus, please contact us on info@snp-nexus.org

Please, enter your institutional email when you run a query - We will notify you when your results are ready.

Full name

Institution

Institutional email (*)

Dataset name

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Human Assembly:

GRCh38/hg38

Single Sample
Multiple Samples

Paste your query in the Text Area below or, alternatively, upload a vcf file or a text file (refer to the User Guide for the input format)
with up to 200000 variants.
Multi-allelic variants are not supported in this version of SNPnexus.

Input file (Max. 20 Mb):

Please, be aware that for large queries and multiple samples, we have to use a low priority queue to avoid blocking other users from using the tool.

⋆ Option 1 - ZIP File:

You can upload one zip file with up to 12 text files using the SNPnexus text format.
Multi-allelic variants are not supported in this version of SNPnexus.
For this option, the filenames are used as sample IDs:

Zip File:

⋆ Option 2 - Text Files:

You can upload one file per sample (up to 12 samples) following the SNPnexus Text format.
Multi-allelic variants are not supported in this version of SNPnexus.
You can specify a sample ID per file uploaded or the filename of the file will be used:

Sample ID:

You can use the pre-filter option to limit the number of variants from WGS variation files. You can select a set of genes or use a curated set from Genomics England or from GENCODE. Alternatively, you can upload a Text file with a set of genes (using ENSG IDs one gene per row):

Select genes:

Include COVID-19 related genes from GENCODE

Include COVID-19 related genes from Genomics England

User details

Query

Pre-filters (Optional)

Annotation Categories Select All