Tutorial

This section explains how to use main tasks for BiERapp:

Creating an account

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

(images/registering.png)

User interface functionality

Upload & manage

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). 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:

(images/filters.png)

• 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)
• Stats. This filter shows several ways of selecting by allele frequency, genotype frequency, number of mendelian errors, presence of indel, % cases or control for dominant/recessive inheritance. BiERapp also manages efficiently missing values.

(images/stats.png)

• Samples. 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. We only have to select the possible genotypes for each sample:

(images/samples.png)

• Control. This filter is based on known population frequencies: Exome Variant Server and 1000 Genomes:

(images/control.png)

• 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.

(images/summary.png)

• 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 this variables and adding information for new variables. (images/variant_info.png)
  • Effect information.

(images/effect_info.png)

• Genome viewer. Selected variants can be visualized from our genome browser:

(images/genome_viewer.png)