iVariantGuide FAQs2022-05-11T14:21:25-04:00

iVariantGuide Frequently-Asked Questions

How do I find a “Deprecated” Analysis2023-05-23T12:07:18-04:00
Question: I went back to analyses that I had previously paid for, opened them and a warning came up for indicated that the analyses were “deprecated” so I hit the re-analyze button only to find that the files are now locked and require payment to open. What is going on and how do I access the analysis I already paid for?
We periodically update our knowledge base with the latest annotations and references. This is necessary in order to offer our users an analysis that uses the most recent knowledge available. This in fact, is one of the main value points that we provide to our users. Just to give you an idea, the sheer data available now is approximatively 4 times larger than what we had 18 months ago. Furthermore, brand new analysis capabilities are added all the time. For instance, during the past year alone we added an extremely powerful network analysis which is able to discover new mechanisms, as well as a very sophisticated upstream regulator analysis. If you have not seen these yet, it would be worth your time to schedule a 30 min phone call for us to show these to you.
When new knowledge becomes available, our platform lets you know by marking your existing analyses as “deprecated”. Thus, you are aware that they are not based on the latest knowledge available in the field. It is better to find this out from us, rather than from the reviewers of your grant or paper pointing out that your analysis does not mention such and such recent discovery. You original analysis is still fully available to you. You can simply close the warning messages at the top by clicking the X symbol at the top left, immediately to the left of the analysis title. Every single piece of information will still be there, as you saw it when the analysis was first performed.
When new knowledge or new analysis capabilities become available, you may or may not choose to analyze the data again, using the latest knowledge and capabilities available. Please keep in mind that updating an existing analysis involves a resubmission of the original data and a complete re-analysis of that data from scratch. If you choose do resubmit the data for a new analysis and you have a valid subscription, this additional analysis will incur no additional cost but it will count as part of your analyses. However, if your subscription has expired, you will need to either renew it or pay for the individual analyses that you wish to have done.

Here is a step-by-step guide to find your old analysis:

  1. Click on the little “i” icon to the right of your file. That “i” stands for information:

2. In the pop-up window, select the previous version you wish to open and click on the date. That will open that particular set of analysis results:

I just registered and I can’t log in. What should I do now?2018-08-23T12:02:46-04:00

Check your email inbox and spam folder. Look for an automatic activation email sent from noreply@apps.advaitabio.com. If it did land in your spam folder, you should add noreply@apps.advaitabio.com to your address book so that future emails are routed correctly (including notifications when your analyses are complete).

Where can I find my API credentials?2018-08-23T12:03:34-04:00

You can generate API credentials on your Advaita Profile page. Once generated, your API ID will always be displayed, but your API secret will only be shown once, so write it down in a safe place! If you lose your API secret, you can reset it by revoking and generating new API credentials. Keep in mind that this will generate a new API ID in addition to the new API secret.

Do you have a User Guide for iVariantGuide?2020-07-07T15:57:48-04:00

Yes. Please use the button to open the Users Guide.

Is there a free trial? What does it mean that my report status is Locked?2018-11-09T17:11:19-05:00

Yes, every new account comes with several demo analyses shared by the Advaita Team. Once you complete your free registration and log in, click ‘Accept Share’ on the demo card, and the demo report will appear in your Reports Table along with any reports you generate. You can use all functionality of iVariantGuide within these demo reports— including creating new filter Presets, exploring Pathway and GO Analysis, and generating the Printable Report. You may upload and analyze your VCF at any time, but you will not be able to access the results until you unlock them via a subscription.

What variant file formats do you support? Do you have any example files I can try?2018-08-27T17:27:57-04:00

Your VCF needs to adhere to the standard format for VCF v4.1 or above. Here is the Specification File, produced by SAMtools. 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.


This VCF file meets the minimum specifications for iVariantGuide.


If your VCF is rejected by iVariantGuide, here are a few things to check:

  • The file should be tab-delimited. If your columns are separated with spaces, do a find/ replace to make sure you have one tab separating each column.
  • All header lines should begin with ##, except the last line of the file header, which contains column headers and should begin with #.
  • The last line of the file header must contain every column shown in the example (line 15), including at least one Sample Name column header.
  • The columns CHROM, POS, ID, REF, ALT give identifying information about the variant. CHROM and POS are mandatory. The others will accept . (period) in place of missing data.
  • iVariantGuide uses the values from the QUAL column as the quality score for each variant call.
  • The FILTER and INFO columns are required to preserve the integrity of the VCF format. FILTER information is displayed in the variant table, and data from the INFO column is ignored, with one exception: if excluded from FORMAT, read depth (DP) will be read from the INFO column. Regardless of how it is used in iVariantGuide, every field in the INFO column needs its own definition line in the header. In the example above, each field that appears in the INFO column is defined in lines 3-11 (shown with ##INFO).
  • The FORMAT column contains the key to parsing the data in the sample columns. iVariantGuide will prioritize genotype data in the order of: PL, GL, then GT.

The Sample Name column headers will be used as the sample names in iVariantGuide. In the example above, there is one sample and it will be called Sample_1 in iVariantGuide.

What if my variant files are in another format like .maf or .tsv?2018-08-23T12:15:26-04:00

There are several free downloadable tools that can convert between those formats and .vcf. They each come with documentation that makes them simple to use.

Is my data secure? Is it HIPAA compliant?2018-08-23T12:16:19-04:00

Yes! Advaita Cloud Systems adheres to the highest industry standards for data security. All data is encrypted during transfer and only you have access to your data, unless you share it. For those customers requiring HIPAA compliance, Advaita offers a HIPAA compliant environment. Please contact sales@advaitabio.com for additional information.

What reference genomes are supported?2018-08-23T12:16:45-04:00

​iVariantGuide currently supports human hg19 and hg38 (GrCh37 and GrCh38).

What sources are used for generating a report?2018-08-23T12:22:52-04:00

We provide annotations from dbSNP, ClinVar, and 1000 Genomes in addition to all sources contained in our KnowledgeBase, iBioGuide. We also provide links to additional information in iBioGuide as well as external sites such as OMIM, MedGen, and more. At this time iVariantGuide does not support user-defined annotation sources. If there is a specific database you would like us to support, please let us know!

Variant Class
Clinical Significance
Functional Class
Allele Frequency
Depth Distribution
Length of Indel
Substitution Types
Chromosomal Location
GO Terms
dbSNP/1000 genomes
input vcf file
input vcf file
input vcf file
Gene Ontology
Can I share my results? What will the recipient be able to see?2018-08-23T12:24:01-04:00

Yes! You may share a report with anyone you wish. They must register a free account to view it, but will have the level of access that you have. If you are sharing a purchased analysis, your sharee will also be able to see premium features such as pathways and GO analyses. You may also associate a filter preset to any purchased analysis and share that preset with the analysis. When sharing, you may also control which of your recipients may re-share the report or whether you want to maintain control over its dissemination. We also provide a stable public link direct to your report in case you wish to share it publicly (e.g. publication).

Can I export data and/or images from my report?2018-08-23T12:24:32-04:00

Yes! Everywhere you see a download arrow within a report, there are data and/or images that may be exported. iVariantGuide also provides a comprehensive summary report that can be printed or downloaded as a pdf. (Paid accounts only.)

How should I cite iVariantGuide?2018-08-23T12:25:29-04:00

Using Advaita Cloud Services’ products or content for any form of publication (e.g. print, electronically) requires researchers to cite them. Please use one of the options below for citations:

  • “The Data (SNPs, insertions, deletions, etc.) were analyzed using Advaita Bio’s iVariantGuide (http://ivariantguide.advaitabio.com)”.
  • LaTeX users may use the following code in a bibtex file: ~\cite{advaita2016}

author = {Advaita, Corporation},
title = {Variant Analysis with iVariantGuide},
month = Apr, year = {2016},
url = { http://ivariantguide.advaitabio.com }

How long does an analysis take?2020-07-07T15:42:29-04:00

Generally, each analysis takes about 15 minutes to complete. If there are other analyses queued ahead of yours, it may take a bit longer. You will receive an email as soon as the analysis is complete.

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