Tutorial

This section explains how to use BiERapp.

User interface functionality

On the top of home page, there are two information options about BiERapp: documentation and tutorial.
After logging in, job names can be visualized on the right of main page and clicking each of them, it is possible to know its variant results.

Upload

The input is a VCF file: individual VCF file for only one sample or multisample VCF file for several samples (families or group of cases /controls).

[HPG Variant] (http://www.opencb.org/subprojects/variant) includes tools to manage VCF files: merging several VCF files in an only multisample VCF, splitting one into several files and retrieving statistics related to variants and samples.

More information about Variant Calling Format.

How does BiERapp work?:

• After uploading VCF file, BiERapp detects variants for all samples.
• Initial results show the whole set of variants. This is a general first view of detected variants. Next step for each user is defining his own strategy of filtering according to his interests.

Filtering options:

There are several filters to define the best strategy of variant selection. It is possible to choose one or several filtering options at the same time:

• Region. Several possibilities to define a region:
  • Only one chromosomal region: 1:1-10000000
  • Several regions (separated by comma): 1:1-10000000, 2:1-10000000
  • Some chromosomes(separated by comma): 4,5,8
• Gene. Only variants for a group of genes. Example: BRCA2,PPL (separated by comma)
• Segregation. This intuitive filter that allows reproducing any familiar pedigree with any inheritance model. Also case-control or sporadic de novo mutational diseases can be analysed in this framework. BiERapp also manages efficiently missing values. We only have to select the possible genotypes for each sample:

• MAF. This filter is based on known population frequencies: Exome Variant Server and 1000 Genomes, including several subpopulations:

• Effect. Selecting one or multiple consequence type.

BiERapp outputs:

• Summary.
  • Global statistics: frequencies about number of variants, indels, snps, biallelic, multiallelic, transitions, transversions, % PASS, Ti/Tv Ratio and average quality.
  • Graphical representation for different consequence type.

• Variants and effects. Detected variants and its effects for all samples.
  • Variant information. BiERApp shows detailed information for each variant: controls MAF, SNP id, PolyPhen, SIFT, consequence type,....
    Clicking drop down buttons, it is possible order this information for any of these variables and adding information for new variables.
  • Effect information for each variant:
• Genome viewer. Selected variants can be visualized from our genome browser:

Creating an account

In addition to run occasional sessions you can have an account in BiERapp. It is free. Once your account is created you can log in into a private session. All the jobs you run will be saved there and will appear in the next session.

To create a new account, you only have to click sign in. It will appear a new window where you can select new account and fill in some fields:

Contact

To report an error or suggestion, please contact us at: babelomics@cipf.es