Welcome to VUStruct

VUStruct Pipeline Case Input and Launch Form

For overview, tutorials and more, visit: VUStruct Home

Please cite: VUStruct: a compute pipeline for high throughput and personalized structural biology

Regrettably, automated launches of the pipeline are offline following ACCRE’s massive /dors filesystem outage on Sept 9..

No timeline for restoration has been announced by Vanderbilt’s IT group. Thank you for your patience. In the meantime, we are happy to run variants for you at our Washington University of St. Louis mirror site. Please email chris.moth@vanderbilt.edu

To launch VUStruct, complete the form below and click at the bottom.

To supply a list of Variants of Unknown Significance (VUS) to the VUStruct pipeline, you may:

Select the Demonstration VUStruct CSV text input option, or

Upload a VUStruct CSV file, or

Upload genomic coordinates for preprocessing, in VCF, Vanderbilt or WUSTL format

Thank you for submitting your variant list to VUStruct!

VUStruct Case Label (4 to 20 characters)(Required)

Enter an ID such as UDN12435678

Data Format(Required)

Select a format to upload a set of VUS (variants of unknown significance)

Vanderbilt-specific Spreadsheet Upload(Required)

Accepted file types: xlsx, Max. file size: 1 MB.

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

VUStruct CSV(Required)

Accepted file types: csv, Max. file size: 1 MB.

Use this format if you already have amino acid changes. Paste a comma delimited set of data… The minimum headers are gene, uniprot ID (unp), mutation (example P35G).

Washingto U.-specific Spreadsheet Upload(Required)

Accepted file types: xlsx, Max. file size: 1 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)(Required)

Accepted file types: vcf, vcf, Max. file size: 1 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 can be reduced to: #CHROM POS ID REF ALT

VCF Upload (GRCh37 coordinates to liftover)(Required)

Accepted file types: vcf, Max. file size: 1 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

Demonstration VUStruct CSV Input

index,gene,chrom,pos,change,effect,transcript,unp,refseq,mutation,genome,inheritance,zygosity
1,COA5,chr2,98608380,G/A,missense,ENST00000328709.8,Q86WW8,NM_001008215.2,P9L,GRCh38,father,heterozygous
2,NAGA,chr22,42067209,C/T,missense,ENST00000396398.8;ENST00000402937.1;ENST00000403363.5,P17050,NM_000262.2,D136N,GRCh38,mother,heterozygous
3,SMYD5,chr2,73218934,C/A,missense,ENST00000389501.9,Q6GMV2,NM_006062.2,A57E,GRCh38,father,heterozygous
4,SMARCAL1,chr2,216447069,G/A,missense,ENST00000357276.9;ENST00000358207.9;ENST00000425815.6;ENST00000430374.6;ENST00000444508.6,Q9NZC9,NM_001127207.1,A588T,GRCh38,mother,heterozygous
5,ONECUT1,chr15,52789080,G/C,missense,ENST00000305901.7,Q9UBC0,NM_004498.2,R269G,GRCh38,father,heterozygous
6,ALAS2,chrX,55017645,C/T,missense,ENST00000650242.1,P22557-1,NM_000032.4,A282T,GRCh38,mother,X-linked
7,ALAS2,chrX,55017645,C/T,missense,ENST00000335854.8,P22557-2,NM_001037967.3,A245T,GRCh38,mother,X-linked
8,ALAS2,chrX,55017645,C/T,missense,ENST00000396198.7,P22557-4,NM_001037968.3,A269T,GRCh38,mother,X-linked
9,AP3D1,chr19,2115592,C/T,missense,ENST00000345016.9,O14617-1,NM_003938.6,V699M,GRCh38,mother,heterozygous
10,AP3D1,chr19,2115592,C/T,missense,ENST00000643116.3,O14617-5,NM_001261826.1,V699M,GRCh38,mother,heterozygous
11,RTEL1,chr20,63688301,G/A,missense,ENST00000370018.7,Q9NZ71-1,NM_016434.3,G546D,GRCh38,mother,heterozygous
12,RTEL1,chr20,63688301,G/A,missense,ENST00000360203.11,Q9NZ71-6,NM_001283009.1,G546D,GRCh38,mother,heterozygous
13,RTEL1,chr20,63688301,G/A,missense,ENST00000508582.7,Q9NZ71-7,NM_032957.4,G570D,GRCh38,mother,heterozygous
14,RTEL1,chr20,63688301,G/A,missense,ENST00000482936.6,Q9NZ71-8,NA,G546D,GRCh38,mother,heterozygous
15,RTEL1,chr20,63688301,G/A,missense,ENST00000318100.9,Q9NZ71-9,NM_001283010.1,G323D,GRCh38,mother,heterozygous
16,SORD,chr15,45069018,CG/C,Frameshift deletion,,Q00796-1,NM_003104.6,Frameshift deletion,GRCh38,mother,homozygous
17,SEC61A2,chr10,12085047,,Deletion,,,,Deletion,GRCh38,de novo,heterozygous

All Pipeline calculations are run from a comma-delimited file like the sample above. This same VUStruct format is created when other formats (VCF, etc) are uploaded and “preprocessed.” The minimum columns are index, gene, effect, unp (Uniprot ID), and mutation when effect=missense

Optional: Your Email address for case report URL and status update

After you click Submit below, you will be taken to the Case Report URL, which you should bookmark. If you enter an email address here, we will also email you the URL, as well as single emails to report any specific technical difficulty, and finally an email to report case completion. We will not share your email address.