Annotation, Visualization and Impact Analysis

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 'Sample BED data' for a self guided tutorial.

Section I. Input Data (Required)

Name your submission (optional):		If name exists, AVIA will add timestamp
*Input Filename:	(?)
	Check ONLY if your input file is a compressed file (zip, tar or gzip) with multiple variant files
-- or --
(?)
*Input format:	VCF4 formatted fileANNOVAR format input (BED)CLC BioHGVSIon Torrent Variant CallerdbSNP identifiers	Check to split multiple alleles on one line into two separate annotations
*Organism and build	Human v37 Human v36 Mouse v38
*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 Protein coding algorithms under "Protein Coding". Click on options below to customize your annotations. Expand/Collapse any category by clicking on the arrows. Check All Annotation Databases --or-- Expand/Collapse All Categories to Customize

Check to annotate using Ensembl instead of RefSeq.

Customize your annotation below:

Protein Coding Select all in Protein Coding

SIFT Scores w/Predictions for SNPs Only Annotation     Polyphen2 Scores w/Predictions **based on Human Var set Annotation     Polyphen2 Scores w/Predictions **based on Human Div set Annotation     Mutation Taster Annotation     Mutation Assessor Annotation     Pre-computed Provean v1.1 Scores from dbSNP Annotation     Combined Annotation Dependent Depletion Annotation     FATHMM Annotation     Variant Effect Scoring Tool Annotation

Disease Related Select all in Disease Related

COSMIC v70 Annotation     Select a version: cosmic70cosmicdbv68   OMIM (gene-centric) Annotation     ClinVar (Default: June 2015) Annotation     Select a version: clinvar_20161128clinvar_20160302clinvar_20150629clinvar_20150330clinvar_20140702clinvar_20131105   Mendelian Clincally Applicable Pathogencity (M-CAP) Score Annotation

Non-coding Regulators Select all in Non-coding Regulators

snoRNA and miRNA annotations Annotation     HMDD Full Annotations Annotation     Linc RNA Annotation     Lncipedia Annotation     SomamiR Annotation     VISTA Enhancers Annotation     ENCODE ChIP Seq Uniform Peaks Annotation     ENCODE Methylation by RRBS Annotation     CpG Islands Annotation     RBP-Var New! Annotation     RegulomeDB v141 Annotation

Targets of Non-coding Regulators Select all in Targets of Non-coding Regulators

Conserved Transcription Binding Sites Annotation     miRNA targets Annotation     microPIR targets Annotation     SomamiR targets Annotation     VISTA Expression Targets Annotation

Known Variations Select all in Known Variations

dbSNP Annotation     Select a version: avsnp147avsnp142snp138snp137

Genomics Datasets Select all in Genomics Datasets

Complete Genomics Genomes Annotation     1000 Genomes Project Annotation     Select a population: ALL.sites.2014_10AFR.sites.2014_10AMR.sites.2014_10EAS.sites.2014_10EUR.sites.2014_10SAS.sites.2014_10   HapMap project Annotation     GWAS catalog Annotation     NCI-60 Annotation     NHLBI-Exome Sequencing Project v2 (ESP) Annotation     Select a population: esp6500siv2_allesp6500siv2_eaesp6500siv2_aa   Exome Aggregation Consortium (ExAC v03) Annotation     Select a population: ExAC_ALLExAC_AFRExAC_AMRExAC_EASExAC_FINExAC_NFEExAC_OTHExAC_SAS   Exome Aggregation Consortium (ExAC v03) Non-TCGA Annotation     Select a population: ExAC_ALLExAC_AFRExAC_AMRExAC_EASExAC_FINExAC_NFEExAC_OTHExAC_SAS   Haplotype Reference Consortium (HRC) Annotation

Genomic Features Select all in Genomic Features

NonB Annotation     Segmental duplications from UCSC Annotation     Predicted Prosite Domains Annotation     Database of Genomic Variants (DGV) Annotation     Repeat Masker Annotation     CytoBand Annotation     FANTOM5 CAGE peaks Annotation     FANTOM5 Enhancers Annotation     FANTOM5 CAGE peaks Annotation     Post-Translational Modifications from PhosphoSite and Phosida Annotation     Post-Translational Modifications from dbPTM Annotation     MutAligner: Somatic mutation hotspots in protein domains in cancer. Annotation

Alternative Splicing and Enhancers Select all in Alternative Splicing and Enhancers

Ensembl63 Splice Events Annotation     ESE Finder Annotation     Tandem Splice Database Annotation

Sequence Mapability and Mutability Select all in Sequence Mapability and Mutability

Encode's Mapability Factor (100mer) Annotation     Uniqueness Factor (35bp) Annotation     Excludable Regions Annotation

Pathway Visualization Select all in Pathway Visualization

Pathview KEGG Network Graphs

Specify your own annotation databases:

Add User-defined Annotation File (?)

There is a maximum upload size of 2G for all uploaded files (including your input file). Please contact us if you have larger files you wish to use on a consistent basis.

General Options:

Include 20bp flanking sequence around mutation in report?  Add your filename to the leftmost column of your output file?  Add zygosity as separate column (1=homozygous, 0=heterozygous) for single patient VCF  Convert final output back to VCF file with Annotations in INFO column (only if original file is in VCF format)  Show all annotations per variant  (?)

By default, your variants will be annotated using Protein coding algorithms under "Protein Coding". Click on options below to customize your annotations. Expand/Collapse any category by clicking on the arrows. Check All Annotation Databases --or-- Expand/Collapse All Categories to Customize

Customize your annotation below:

Known Variations Select all in Known Variations

dbSNP (Default: v142) Annotation     Select a version: snp142snp137.vcf

Genomic Features Select all in Genomic Features

Simple Repeats from TRF Annotation     CpG Islands Annotation     Segmental duplications from UCSC Annotation     Post-Translational Modifications from dbPTM Annotation

Protein Coding Select all in Protein Coding

SIFT4G Scores w/Predictions for SNPs Only Annotation     Pre-computed Provean Scores from dbSNP Annotation

Conservation Scores Select all in Conservation Scores

PhyloP Scores across 60 organisms (sumSquares) Annotation     phastConsElements60way Annotation

Databases Converted from Human Select all in Databases Converted from Human

Polyphen2 Scores w/Predictions **based on Human Div set Annotation     ClinVar (Default: June 2015) Annotation

Pathway Visualization Select all in Pathway Visualization

Pathview KEGG Network Graphs

Specify your own annotation databases:

Add User-defined Annotation File (?)

There is a maximum upload size of 2G for all uploaded files (including your input file). Please contact us if you have larger files you wish to use on a consistent basis.

General Options:

Add your filename to the leftmost column of your output file?  Add zygosity as separate column (1=homozygous, 0=heterozygous) for single patient VCF  Convert final output back to VCF file with Annotations in INFO column (only if original file is in VCF format)  Show all annotations per variant  (?)

Section III. Prioritization

Function based Prioritization of Sequence Variants (FunSeq2) workflow

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.