iVariantGuide Release Notes2018-10-30T12:30:21+00:00
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iVariantGuide Release Notes

Release Notes – Winter 20182018-08-25T09:33:07+00:00

On January 12, 2018, Advaita released a major updates to its platform, with improvements to iPathwayGuide, iVariantGuide, and iBioguide.

IMPROVEMENTS

The Advaita Knowledgebase was updated to version 1711 and now includes:

  • 3 organisms: homo sapiens, mus musculus, rattus norvegicus
  • 213,390 Genes
  • 1,933 Diseases
  • 44,976 GO terms
  • 4,791 Drugs
  • 955 Pathways
  • 5,710 miRNAs
  • 3,161,730 References
  • For a complete list of databases and versions, please see report information within each application.

NEW FEATURES

  • iVariantGuide: API Client now accepts multi-sample analyses
  • Improvements to account registration page to ensure proper organization affiliation.

BUG FIXES

  • iPathwayGuide: Improvements to parsing of CuffDiff-formatted files to maintain association of phenotype labels. Fold changes and p-value parsing remains untouched.
Getting Started in iVariantGuide2018-08-25T09:51:55+00:00

Uploading and analyzing data is easy.  Here is a quick video tutorial explaining how.

1. SELECT/ UPLOAD FILE
The first step is to upload your VCF file containing all of the variants and samples you want to analyze. Here are a few tips:

  • Make sure the file meets the specs for VCF v4.1 or higher. Especially:
    • It contains each of the following columns: CHROM, POS, REF, ALT, FILTER, QUAL, INFO, FORMAT, and at least one Sample
    • All INFO and FORMAT tags are defined with their own line in the header
  • There is no limit to the number of variants or samples in your file, but very large files (> 1M variants) could have a slower browsing experience.
  • Don’t have your data ready? We have sample datasets available. Grab a sample file and try it… it’s easy!

Once uploaded, select the checkbox next to the file you’d like to analyze. You will then be prompted to verify the reference assembly and select the type of analysis you wish to perform, including:

  • Case v Control (Group vs Group)
  • Tumor/ Normal (Paired Samples)
  • Pedigrees (Trio, Quad, and larger families)
  • Individual Samples

Lastly, iVariantGuide allows you to pre-filter your variants by quality, read depth, and FILTER flags. If there are certain quality control measures you know you’ll apply anyway, this step will help to focus the variants in your analysis to only those you are confident of, while ensuring a more favorable browsing experience.

2. ADD SAMPLES TO GROUPS

You may assign information to each sample in the file (sex, group, parents) in the page or by uploading a file containing the necessary information. You may also re-name samples (in case the VCF sample names are not easy to read). iVariantGuide accepts two formats for sample information: ped for pedigree analysis and txt for group vs group and tumor/ normal analyses. For a description and example of each file format, see below.

File Formats for Specifying Sample Info

  • PED: a space or tab-delimited file with at least 6 columns, and one row per sample. Read more here and here. Download an example file.
  • TXT: a tab-delimited file with one header row and one row per sample.
    • To use this format, download the example file and open it in Excel or another spreadsheet program. Then replace the example values with the following sample information from your own data. The columns are as follows:
      • sample: the sample names from the VCF file
      • name: the sample names to display in iVariantGuide (if blank, will default to values in sample column)
      • sex: male or female. case-sensitive, if blank will be unknown.
      • paternal: sample name of father (if known)
      • maternal: sample name of mother (if known)
      • group: name of group (for group vs group and tumor/ normal analyses, this column must contain exactly two different group names)

IMPORTANT NOTE: Check the order of your samples! The first sample in the PED file is always the proband, and the first phenotype found is Affected. The second phenotype found (the first row with a phenotype different from that of the proband) is Unaffected, and the third is Unknown. For TXT files, the first group found is Tumor/ Case and the second is Normal/ Control.

3. CREATE REPORT

On the last page you can review the selections you made so far, and give your analysis a Title and Description. Once satisfied, click submit. Each dataset takes about 15 minutes to analyze. You will get an automated email as soon as your analysis is complete.

Advaita Releases API client for iVariantGuide and iPathwayGuide2018-10-09T14:41:41+00:00

With Advaita’s latest update to its applications and knowledge base, Advaita updated its API for iVariantGuide and iPathwayGuide.

An API or (Application Program Interface) is a set of routines, protocols, and tools for building software applications. An API specifies how software components should interact. Advaita’s API is designed for advanced users of iPathwayGuide and iVariantGuide who would like to streamline their data processing and bypass the UI for submitting data.

Advaita’s API is designed to take advantage of the AWS EC2 environment and allow users to submit one to several datasets in rapid succession. Results from the application are still viewed in the application and are just as informative.

The API documentation and links are viewable at: ​https://hub.docker.com/r/advaitabio/api-client/

API access and support is available to subscribers who have opted for API access to either iPathwayGuide or iVariantGuide customers. If you would like to add API access to your existing annual subscription, please contact us at sales@AdvaitaBio.com for additional information.

Winter 2017 Release Notes2018-08-25T09:59:16+00:00

On February 27, 2017, Advaita released a major updates to its platform. These are the release notes.

IMPROVEMENTS TO: iPathwayGuide, iVariantGuide, iBioguide, and the Advaita Knowledge Base

  • Changes to AWS services in preparation for HIPAA compliance
  • Updated knowledge base to version Advaita KB v1702, which includes the following data sources and versions:
Database Version iPG Annotations iVG Annotations
KEGG Release 81.0+/01-20, Jan 17​ Pathways, Diseases, Drugs​ Pathways
Gene Ontology ​2016-Sep26 GO Terms GO Terms
Targetscan Targetscan v7.1 miRNA Target Genes miRNA Target Genes
MIRBASE MIRBASE v21,06/14 miRNA Sequences
dbSNP (incl 1k genomes) Build 149 Minor Allele freq.
RefSeq Release 71 July 2016 Impacted Transcripts
ClinVar Dec 1, 2016 Clinical Significance
​SNPEff ​v4.1L Predicted Impact

IMPROVEMENTS TO iPATHWAYGUIDE

  • NEW FEATURE! Onboarding carousel with top user benefits
  • NEW FEATURE! API (Premium feature)
  • Bug fix: genes selected in Genes Table on Pathways page are now highlighted on pathway map

IMPROVEMENTS TO iVARIANTGUIDE

  • Improved error messaging for sample upload & report creation
  • NEW FEATURE! Versioning: each report now shows which version of the Advaita Knowledgebase was used to annotate the sample. Outdated reports may be updated when viewing Report Info: either on the Reports page or from within the report itself. As is true for other Advaita applications, only the report owner may update it.

IMPROVEMENTS TO iBIOGUIDE

  • Updated to use AKB v1702
iVariantGuide Commercial Release Notes2018-08-25T10:02:40+00:00

11/1/2016

The Commercial Release of iVairantGuide is here! With this commercial release we now have the following enhancements from the last Beta:

  • Redesigned uploading and intake navigation work flow with onboarding queues
  • Improved navigation and selection on visual filters/graphs
  • Improved sharing capabilities:
    • View share history
    • autofill prompts for often-used email addresses
    • Ability to associate filter presets to shared report
    • Ability to associate filter presets to public link (anyone can see what you see)
  • Improved tooltips and onboarding
  • Improved pathway and GO analysis with p-value ranking and advanced correction factors
  • UI improvement
  • User profile page
  • API credentials
  • Initial API (Premium Feature)
  • Printable Summary (Premium Feature)
  • Improved Pathway and GO Analysis (Premium Feature)
  • Harmonization of labeling and naming conventions
  • Numerous bug fixes and security enhancements
iVariantGuide Beta 2 Release Notes2018-08-25T10:04:45+00:00

9/6/2016

In the pre-commercial release of iVariantGuide the following issues have been addressed:

  • Redesigned uploading and intake navigation work flow with onboarding queues
  • Improved navigation and selection on visual filters/graphs
  • Improved sharing capabilities:
    • View share history
    • autofill prompts for often-used email addresses
    • Ability to associate filter presets to shared report
    • Ability to associate filter presets to public link (anyone can see what you see)
  • Improved tooltips
  • Improved pathway and GO analysis with p-value ranking and advanced correction factors
  • UI improvement
  • User profile page
  • Introduction of subscriptions (free during beta) to see premium features
  • Redesign of processing engine to paralellize analyses
  • Improved filtering speed
  • Harmonization of labeling and naming conventions
  • Numerous bug fixes and security enhancements
May 2016 Release Notes2018-08-25T10:05:56+00:00
  • Redesigned uploading and intake navigation work flow
  • Improved navigation and selection on visual filters/graphs
  • Improved tooltips
  • Redesigned notification of filter presets when navigating away from variants page
  • Harmonization of labeling and naming conventions
  • Numerous bug fixes and security enhancements
Beta Release Notes2018-10-11T11:29:30+00:00

4/11/2016

  • Analyses are currently limited to single sample analyses. Multi-sample analyses are in development.
  • Input file size is limited to ~100mb for now.
  • Input files must be .vcf or .vcf.gz version 4.1 or later; reference genomes hg19 (GRCh37) and GRCh38 are supported.
  • Supported filters include by quality, read depth, genomic region, variant class, predicted effect, clinical significance, and impact score.
  • Filter combinations may be saved as “Presets” for later use with new data sets.
  • Detailed variant view includes links to: iBioGuide, dbSNP, OMIM, MedGen, PubMed, and more.
  • View variants in context of impacted pathways. Pathway view highlights affected genes and provides ability to model miRNAs and drugs.
  • View variants in relation to GO terms. Navigate upstream and downstream to identify specific ontology terms.
  • Share reports with individuals or publicly.
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