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Analysis of Genomic Variations with AVIA

What's New

A new look is coming to AVIA!! Stay tuned...



October 3, 2016

We have several minor changes in the current version of AVIA.
  • Mouse annotations are available!! We have added a limited subset of mouse annotations for mm10. For gene annotations, we used RefSeq annotations. We have also used UCSC's LiftOver tool to convert HUMAN annotation databases to mouse genome coordinates for Polyphen2 Scores (div) and ClinVar. If you have any other mouse annotations that you would like us to add, please click here.
  • ANNOVAR updates ANNOVAR gene annotations will now include all annotations (not just by precedence). Previously, if a mutation hit within a coding mutation for a particular transcript, but an intron in another transcript, it would only display the coding transcript. It can now show all.
  • Multiple configurations file Users may now have multiple configuration files. This is partly due to the addition of the mouse annotations
  • You can now name your submission It was confusing with that long submission ID, so now we allow you to name your submission. If it already exists, AVIA will tag it with the date. But as always, these IDs will start with "viz-"
  • Now accepting dbSNP identifiers




January 12, 2016

Added ability to annotate multiple alleles for the same position for VCF files only. When you change the dropdown menu for input format to VCF, a checkbox will appear for split multiple alleles into separate annotation lines. This will be useful for variant based annotations such as dbSNP and sequencing projects such as ESP, ExAC, etc.



December 15, 2015

Bug Fixes!! We noticed and fixed some bugs in the pages and annotations. (Only the ones in red impacted the actual annotations)
  • Fixed issues with small datasets not being displayed on the website
  • Fixed issue with dbSNP annotations (avsnp142)
  • Fixed issue with DAVID API and reinstated the DAVID Ontology tab on the results page
  • Fixed issue impacting the users' ability to select versions of certain databases and datasets from sequencing projects
December 8, 2015

Server upgrades took place on December 2 and we were experiencing some issues, but they have been fully resolved. If not, please contact us. We updated our OS and security certificates, but none should impact annotations. You will now notice that our URL has changed slightly to https://avia-abcc.ncifcrf.gov.



September 5, 2015

We have disabled the DAVID clustering component of AVIA due to server issues. We apologize for any inconvenience. You can still visit their website by clicking here. Updated 12/15/15 DAVID services have been restored!!!



August 24, 2015

Results by gene can now be downloaded! Please see the link here and select "Get gene based annotations" from the drop down menu!! These annotations are also available on your results page under the "Gene Annotations" tab.



May 18, 2015

We've modified some of our policies and made some bug changes! Please find those changes outlined below:
  • ***Policy Change*** Multi-Zip files: Due to the number of zipped files, we have disabled users' ability to do exploratory analysis on the web. Instead, they will be emailed a link to the page where they can download full annotations! This will allow batch users to get results much faster!
  • New inputs allowed: For Protein HGVS, we now accept Ensembl IDs (gene,transcript, or protein)! Any conversions which failed will now be available in the "Download All" archive in the file called "notconverted.txt". Just be sure to click the "Input is Ensembl IDs"!!
  • Fixed bugs with inconsistency between large vs small files (not data, just the column names and order)
  • Databases Updates!!
    • Updated dbSNP, ESP and clinVar. (Thanks to ANNOVAR developers!)

      For more information, please see our databases page by clicking here
    • **For maintenance purposes, dbSNP no longer has het Frequency
    • Added ExAC (Also thanks to ANNOVAR developers!!
      • This also allows users to specify population
  • Added the ability to pick the version of databases on the main submit page. By default, the most recent will run.




April 9, 2015

We recently published in Bioinformatics!



March 10, 2015

We added extended our PDB structure library to include known partial structures from PDB. Now, you can view protein mutations in the context of protein structure and have a side by side comparison of the original amino acid and its properties!



February 23, 2015

The following changes were made:
  • The gene based exploratory tab has been improved. Selection of gene will pull up all available data for that gene.
  • KEGG Pathway/PathView integrated maps are interactive and now link out to KEGG page for the gene clusters. Hovering over the gene will also show the damaging scores for genes in that cluster
  • The Basic annotation tool was added for users who just want the annotation without the visualization or extended gene interactions




January 26, 2015

We recently presented posters at the "Cancer and Epigenetics" Conference in Keystone, CO. Check out our poster! AVIA poster @ Keystone



November 19, 2014

We added the ability to submit zipped files with multiple input files (of the same type) to AVIA. You will recieve an email for each input in the compressed archive. Users may be limited by the number of submissions. Please make sure to check the correct box! The size of the input file is still limited to <1.0 GB.



October 1, 2014

We made some changes to the web interface/back end databases to include the following:
  • We updated all databases from ANNOVAR to ljb26 and added the CADD, FATHMM, and VEST databases. COSMIC and the 1000G file were also updated. If you wish to annotate with previous versions of databases, please contact us!
  • We also changed the page so that larger variant datasets could be viewed and explored on the web. Only a those variants "of consequence" will be displayed on the web. Downloads will still have your entire dataset.
  • All Ensembl requests have conversions to RefSeq Gene Symbols for consistency
  • Sample VCF file is now included
  • Documentation on all prioritization steps is completed




July 21, 2014

Official Launch of AVIA v2.0! We have greatly improved the usability and the look and feel of the AVIA page. Please contact us if you have any problems or have any comments. Feedback is greatly appreciated!!



June 14, 2014

We added a separate converter and gene access page so users can take advantage of the secondary features of AVIA without submitting a variants file. Please visit the new page by clicking on "File/Data Converter Tools" under "General Tools" or by clicking here.



June 4, 2014

Gene based annotations page added as a separate component. Please visit the page by selecting the "Gene-based annotations" on the drop down menu under "General Tools" or with the link here.



Feb 14, 2014

Video Tutorials are available!!! We have added new and improved tutorials. Click here to go to the tutorials page.



Jan 14,2014

We have added more gene-based annotations! We added Metabolome data from HMDB, Protein Interactions from BioGrid, gene expression data from GSEA for all users. Drug information from PharmGKB is also provided but restricted to NIH users only due to licensing agreements. Check out the added information on the sample results page here under the "Gene-based annotations" tab.



Nov 7, 2013

AVIAv1.0 manuscript is accepted into the journal Bioinformatics!! Check out the advanced copy by clicking here!



August 2013 Changes to the website
  • Improved results page with more annotations
  • New About page
  • New Comparison variant annotation page




January 21, 2013 Changes to the website
  • Set up Configurations Page Added
  • Cascade filtering Page Added
  • New databases updated and added
  • Database Information Added to the website
  • New results pages with database information
  • Streamlined the navigation pages
  • ** Tutorials ** to guide you through the site
  • You may choose to wait for results (up to 5 minutes) instead of waiting for email notification.
  • Sample data is now available
September 26-29, 2012

We recently presented posters at the Beyond the Genome (Boston, MA) and Common Diseases (Rockville, MD) conferences.

AVIA poster

September 11, 2012
  • Added flanking sequence
  • Added predictions to SIFT and polyphen
  • Added new feature miRNA impact analysis
  • Added 1000Genomes databases
August 8, 2012
  • Added Additional Features and Visualization
June 1, 2012
  • Launch of the AVIA website