VUStruct

Welcome to VUStruct!

As of January 2, 2024, Vanderbilt’s ACCRE cluster is experiencing very slow job launches, due to a holiday software upgrade. We will update this advisory as we learn more

VUStruct analyzes missense variants for your ‘case’ of interest, in context of automatically selected 3D protein structures.

VUStruct Pipeline Case Input and Launch Form

For detailed documentation, tutorials and more, visit VUStruct Home

To launch VUStruct, enter a name for your case, and input variants of unknown significance (VUS) in either:

Genomic coordinates in VCF, Vanderbilt, or WUSTL format (from which missense variants are automatically determined)
or

Comma-delimited list of Uniprot Sequence IDs alongside missense amino acid variants of interest. (Genomic conversion is not performed)

VUStruct Case Label(Required)

Enter an ID such as UDN12435678

Data Format(Required)

Select a format to input VUS (variants of unknown significance)

Vanderbilt-specific Spreadsheet Upload(Required)

Accepted file types: xlsx, Max. file size: 255 MB.

This upload only supports Vanderbilt’s unique UDN variant spreadsheet. To proceed, click [Choose File] and select a .xlsx file from your computer.

Washingto U.-specific Spreadsheet Upload(Required)

Accepted file types: xlsx, Max. file size: 255 MB.

This upload only supports Wash U’s unique UDN variant spreadsheet. To proceed, click [Choose File] and select a .xlsx file from your computer.

VCF Upload (GRCh38 coordinates)

Accepted file types: vcf, vcf, Max. file size: 255 MB.

VCF is a tab-delimited format. Your file will be filtered for missense variants using the Ensembl VEP Your VCF file tab-delimited headers should be minimally: #CHROM POS ID REF ALT

VCF Upload (GRCh37 coordinates to liftover)

Accepted file types: vcf, Max. file size: 255 MB.

VCF is a tab-delimited format. Your GRCh37 file will be first “lifted over” to GRCh38 with the UCSF tool. Then, it will be filtered for missense variants using the Ensembl VEP Your VCF file tab-delimited headers should be minimally: #CHROM POS ID REF ALT

Comma Delimited Missense Variants

Paste a comma delimited set of data… The minimum headers are gene, unpiprot ID (unp), mutation (example P35G)

Optional Additional Inheritance Data (zygosity) for Digenic Analysis

Paste comma-delimited data per tutorial. For each gene, you can indicate whether a variant was inherited from father, or bother, or both.