iVariantGuide Tutorials2018-10-30T12:29:43+00:00
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iVariantGuide Tutorials

Getting Started in iVariantGuide2018-08-23T15:10:22+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.

Graphical Filtering in iVariantGuide 2.02018-08-23T15:12:31+00:00

Explore all of the options for customizable graphical filtering in the brand new iVariantGuide. (2:03)

Creating New Analyses in iVariantGuide 2.02018-08-23T16:52:15+00:00

We’ve released a brand new version of iVariantGuide. Here are step by step instructions for uploading and analyzing your VCF files. (2:05)

Pathway Analysis of High-Priority Variants2018-08-23T16:54:00+00:00

​The Pathway Analysis module in iVariantGuide allows you to explore the pathways that are impacted by high-priority variants. See how you can use this powerful module to identify biological links between variants or make new functional hypotheses and design experiments to test them.

Case v. Control in iVariantGuide Webinar2018-08-23T16:55:29+00:00

In this video, Dr. Cordelia Ziraldo walks you through the steps needed to do a Case v Control analysis in iVariantGuide using RNAseq-based variant data in breast cancer subtypes. Dr. Ziraldo shows you how to identify which systems (pathways, biological processes, molecular functions, and cellular components) and the mechanisms that may be implicated in these breast cancer subtypes.

Gene Ontology Analysis for variants in iVariantGuide2018-08-23T16:58:28+00:00

Gene Ontology (or GO) Analysis identifies the biological processes, molecular functions, and cellular components that are likely affected by your high-priority variants. See how iVariantGuide leverages state-of-the-art algorithms to drill down to the specific biological phenomena relevant to your data.

Filtering Variants in iVariantGuide2018-08-23T16:59:45+00:00

iVariantGuide’s dynamic, graphical filters help you take your variant analysis to the next level. Find hidden correlations when visualizations of every annotation source update with every new selection you make.

How to Input Variant Data2018-08-23T17:00:49+00:00
Getting Started with iVariantGuide2018-08-23T17:02:26+00:00

Uploading data:

iVariantGuide accepts variant call files meeting the following criteria:

Type: .vcf OR .vcf.gz
Size: .vcf less than 100MB, vcf.gz under 20MB
Version: .vcf 4.1 or later
Assembly: reference genomes hg19 (GRCh37) or GRCh38

Creating analyses:

Start in the top right corner of your reports page. You may create a report from one of your available samples or upload a new sample.
Click upload to add a new sample. Browse to select your VCF and choose the reference genome assembly. Once your data is uploaded and pre-processing is complete, summary statistics appear on your screen. If you are satisfied, enter a title and description and click create.

Explore:

You will automatically receive an email as soon as your analysis is complete. When the status bar is green, your report is ready to start exploring!

​Share:

You may enable a public link to share with anyone or enter an individual email address to send a private link.

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