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fgardos edited this page Dec 31, 2013 · 87 revisions

This section explains how to use main tasks for BiERapp:

Creating an account

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:

  • Region.

  • Gene.

  • Stats.

  • 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:

  • Control. This filter is based on known population frequencies

  • Effect.

  • Predicted pathologic effect:

  • Consequence types:

BiERapp also manages efficiently missing values.

BiERapp outputs:

  • Summary: global statistics and a graphical representation for consequence type.
  • Variants and effects: detected variants and its effects for all samples.
  • Genome viewer: selected variants can be visualized from this genome browser

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