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Tutorial

Start using Variant

There are two ways to access Variant tool:

  • Through an annonymous account which does not need any registration, or
  • a user account which need a previous free registration.

To enter either one of the two options click on the Sign in button located at the top right part of your screen:

Accessing with an anonymous account

With this session you are able to work normally (upload your data, process it, download your results, …) with a maximum of 1GB of space to store your jobs.

It is important to bear in mind that this kind of session does not store your jobs in new sessions. If you close your browser window all jobs and data stored will be lost. To avoid this, just register and you will be able to store all jobs in your user account.

Accessing with a user account

Creating a user account has some advantages against the anonymous login. By login with you own account you will be able to store your jobs and data and access them whenever you want. After login out all your projects are stored in our servers with your account, so if you login again with a new session or from another computer your data will remain in the same place.

To create a user account just select New account in the Sing in panel panel and fill the registration form with the information requested.

By summiting your e-mail and password, Variant home page appears with your session on.
Now, you can start working! And all your jobs and data will be saved for the next session if you logout.

Analyze your variants file

To start using Variant clik on the Variant effect link at the top left of the screen and automatically you will redirected to the form page.

Upload your data

Variant has a unique data entry point in its Upload Menu.

By accessing to this form you will be able to upload any variant file you want to analyze using Variant. One single file can be uploaded at a time.

  1. Select your data type: Select the file format your variants file (GFF, BED or VCF).
  2. Some additional data: It is mandatory to enter a Data name to identify the file. This is the name that will be displayed afterward in your job list and projects. Other optional description fields are available.
  3. File origin: Click on Open file to select the file to upload.

Finally, click on Upload to finish and wait (do not leave the page) until the process has been completed.

Select your file

By clicking on Browse file you will be able to select the uploaded file.

Filtering options

If you are only interested in analyzing some particular variants instead of the whole file, here you can indicate some filtering parameters:

  • Region: To retrieve information of variants located in a particular region, just introduce the location using the structure chromosome:start-end. You can specify several regions using comma "," or new line. Example: 2:356734-379530,21:200000-300000.
  • Gene list: Filtering the analysis for specific genes is also possible. Insert the name or ID of the genes you are interested using comma or new line to separate them. In order to avoid losing information of variants located at surrounding regions (such as promoters), 5000 nucleotides upstream and downstream from the start and the end, respectively, of each gene are included in the analysis.
  • Only SNPs: Check this option if you just want to get information about known Single Nucleotide Variants (SNPs) stored in dbSNP. Note that this kind of variants are at least in the 1% of the population.
  • VCF Info: Filter the analysis just for those variants that fulfill any specific parameter specified at the VCF INFO field.
  • VCF quality: Specify a minimum quality of your reads.

Output options

Variant permits the user to retrieve just variants with an specific consequence type. Use check-boxes to indicate the consequence types you are interested in.

Run

Insert a name for this job and click Run. The job will appear at the Jobs and Data list panel. Wait until the job is colored green to click and check your results.

Check your results

The results page contains links to the output of the analyzed variants. All sections of the output are described below.

1. Input

This section is a reminder of the file submitted to run the analysis.

2. Summary

This section links three files:

  • Filtered Variants: When filtering options (i.e. region, gene, quality, ...) have been set in the input form, this file contains a new filtered VCF with the specified conditions. Otherwise, the VCF will be the same as submitted.
  • Genes with Variants: File containing a list of genes where variants have been found.
  • Consequence types histogram: A two-column summary file with the number of the variants for each consequence type.

The summary pie chart summarizes the content of the variant file.

3. Variants by Consequence Type

In this section, users can download all reports generated for the submitted variants. All_variants.txt file contains the complete report for all variant. The rest of the files contain reports for the specified consequence types. Between brackets you will find the total number of entries found for each consequence type.

All reports contain the same columns. See here for further information about output columns.

4. Consequence Type by variants

In this section, you can download consequence_types_by_variants.txt file containing a two-column file containing:

  • Chromosome : Position - Alternative_allele
  • List of consequence types reported for this position.

One of the most interesting outputs is the Genome Maps browser. The viewer places your variants on the genome permitting the selection and visualization of different tracks of biological information.

Users can visualize specific variants easily using the Variant filter tool. Click there, select a gene or a consequence type and, automatically, all variants will appear in the widget. By clicking in any of the reported variants the viewer will be redirected just to this position.