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)
- 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:
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.