3. myVCF features

myVCF is designed as a tool for browsing and visualizing mutational data coming from NGS technologies, including Whole-Exome and -Genome sequencing as well as target resequencing.

Several features have been implemented to help the end-user in the navigation and the exploration of his project. In the next paragraphs you will find the description of principal features available in myVCF.

3.1. How to query a project database?

The search engine in myVCF is very versatile. Once you are in a project homepage, you can query the database by searching for:

  1. Gene name (Official Gene Symbol)
  2. Genomic region (1:20000-200100)
  3. dbSNP ID (rs324239)
  4. Variant (1-456783-456783-A-T)

3.1.1. Gene/Region view

Basic gene/region search will generate a Gene page composed by:

  • Table containing the mutations found in the gene/region
  • Mutation plot showing the distribution of the mutations grouped by their functional consequence.

Here we described a simple gene search example

3.1.2. Variant view

Variant view directly connectes the single variant with the additional information contained in the VCF file uploaded and stored in myVCF database.

The variant page links additional information about the allele frequency of the searched variation by interrogating all the principal population frequency database:

  • ExAC
  • ESP
  • 1000Genomes

Data from those database will be automatically displayed in the page.

3.2. VCF metrics summary

myVCF can also generate a global VCF summary report considering several metrics and information.

You can generate this report by clicking on the Summary button summary_button


The first time you load the summary statistics the process will take several minutes, especially for exome/genome projects. All following loadings will be very fast thanks to the system saving in the cache that speeds-up the process. Cache memory will be removed once the application is closed.

The VCF quality report consists of several statistics and plots all-in-one page. You can export separately each plot as single images.

Here, some example of the statistics generated:

  • Number of variants and the distribution of mutation across samples
summary 1
  • Variant quality distribution
summary 2
  • Variant distribution across chromosomes stratified by functional consequence
summary 3
  • Variant functional consequence distribution as pie chart
summary 4

3.3. Add sample groups

Most of the times, exome and target sequencing projects, are performed to understand the genetic difference between two or more group of samples that belong to a particular phenotype or hold some features of interest according to clinical data.

With myVCF you can easily define samples groups in order to filter and export mutations that are present only in certain samples defined by the group.


This feature is available only for human-based and annotated projects

To define and add groups in specific project, follow these steps:

  1. Click on DB settings page from the project homepage
  2. Go to Setup Groups section
  3. Define a group name and select the sample ID that you want to include in the group select_groups
  1. Save group by clicking on Save group button
  2. You can verify the correct group definition by looking at the Available group lists table.

Now you can apply filters on mutations/region results by your sample group definition.

3.4. Change default columns view

By default myVCF visualizes a set of columns in the gene/region view composed by the principal annotation given by the VCF file.

You can change the default view by accessing to the DB settings page dbcolview_button

You will be redirected to the preferences page and you can select which columns will be displayed in the Gene/Region table.

db columns

To save the column view modified by the user, click on Save changes save_changes