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Upload Parameters for AVIA Analysis

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Analysis of Genomic Variations with AVIA

AVIA Annotation and Visualization Request

In this tool, users will be able to annotate their data with publicly available databases, as well as upload their own databases. Users will also have the opportunity to visualize each of these databases as tracks within Circos.  If a gene list is specified in Section II, the highlight and filter options only apply to the Circos visualization.

Please read our FAQ or Tutorials for detailed information.  If you do not have any data to start with, click on the button below labeled 'Click here for sample data' for a self guided tutorial.

Section I. Input Data (Required)

A field with an asterisk (*) before it is a required field.

  (?)
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Input format:
*Organism and build  Check to use Ensembl annotation instead of RefSeq.
*E-mail address:
You will be notified by email when the process is complete
*Confirm E-mail address:
 

Section II. Annotation and Visualization Parameters

By default, your variants will be annotated using SIFT and Polyphen2. Click on options below to customize your annotations. Expand/Collapse any category by clicking on the arrows.
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Customize your annotation below:
 Protein Coding Select all in Protein Coding
  SIFT Scores w/Predictions for SNPs Only Annotation Visualization
  SIFT NMD Prediction for Indels Only
**takes about 20-30 minutes for ~1500 Indels
Annotation Visualization
  Polyphen2 Scores w/Predictions
**based on Human Var set
Annotation Visualization
 Disease Related Select all in Disease Related
 Non-coding Regulators Select all in Non-coding Regulators
  snoRNA and miRNA annotations Annotation Visualization
  HMDD Full Annotations Annotation Visualization
  Linc RNA Annotation Visualization
  Lncipedia Annotation Visualization
  SomamiR Annotation Visualization
  VISTA Enhancers Annotation Visualization
  ENCODE ChIP Seq Uniform Peaks Annotation Visualization
  CpG Islands Annotation Visualization
 Targets of Non-coding Regulators Select all in Targets of Non-coding Regulators
  Conserved Transcription Binding Sites Annotation Visualization
  miRNA targets Annotation Visualization
  microPIR targets Annotation Visualization
  SomamiR targets Annotation Visualization
  VISTA Expression Targets Annotation Visualization
 Known Variations Select all in Known Variations
  dbSNP (build 137) Annotation Visualization
 Genomics Datasets Select all in Genomics Datasets
  Complete Genomics Genomes Annotation Visualization
  1000 Genomes Project updated April 2012 Annotation Visualization
  HapMap project Annotation Visualization
  GWAS catalog Annotation Visualization
  NCI-60 allele frequencies Annotation Visualization
 Genomic Features Select all in Genomic Features
  NonB Annotation Visualization
  Genomic Duplications from UCSC Annotation Visualization
  Predicted Prosite Domains Annotation Visualization
  Database of Genomic Variants (DGV) Annotation Visualization
  Repeat Masker Annotation Visualization
  CytoBand Annotation Visualization
 Alternative Splicing and Enhancers Select all in Alternative Splicing and Enhancers
  Ensembl63 Splice Events Annotation Visualization
  ESE Finder Annotation Visualization
  Tandem Splice Database Annotation Visualization
 Sequence Mapability and Mutability Select all in Sequence Mapability and Mutability
  Encode's Mapability Factor (100mer) Annotation Visualization
  Excludable Regions Annotation Visualization
Select the resolution of your Circos plots:
Specify your own annotation databases:
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General Options:

Section III. Filter Using Genelist (optional)

By clicking this box, I am verifying that I have read the full disclaimer and I fully understand that the information provided for me by AVIA is for research purposes only. The ABCC, FNLCR, and the NIH or any of the linked websites do not approve use of this information for diagnostic purposes.