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Welcome to the BiERapp wiki!
BiERapp is an interactive web application for assisting in gene prioritization in whole exome sequencing (WES) experiments. BiERapp is mainly oriented to disease gene finding in Mendelian disorders, although it can be applied to other contexts, such as case-control comparisons. BiERapp has been used by the BiER team (Bioinformatics for Rare Diseases) in different versions during the last year for the analysis of more than 1000 exomes of patients of more than 70 different inherited pathologies, produced by the Spanish Network for Research in Rare Diseases (CIBERER) and the Medical Genome Project (MPG)
BiERapp uploads standard VCF formats and provides different filtering options for the variants based on known population frequencies, predicted pathologic effect, consequence types, etc. Its most interesting feature is an intuitive filter that allows reproducing any familiar pedigree with any inheritance model (including incomplete penetrance) and facilitates the selection of variants (and genes with deleterious variants) segregating along the family. Also case-control or sporadic de novo mutational diseases can be analysed in this framework. BiERapp also manages efficiently missing values.
BiERapp is an open source tool based on HTML5 and javascript. The application has been developed in javascript with the Ext JS framework. The Front-end has been developed using the Bootstrap framework. BIERapp uses a fast and optimized indexing and annotating system based in Sqlite for queries. The relevant information on genes, variants, features, etc. used for the prioritization is remotely stored (and keep updated) in CellBase and is provided through highly efficient web services.
BierApp has been designed with these goals in mind:
- 100% web-based using open standards such as HTML5 and SVG. No plugins or other technologies such as Flash or Java Applets are needed.
- To avoid privacy and confidentiality issues genomic data are analysed at user's side.
Recent advances in high-throughput sequencing technologies have made it possible to sequence whole genomes at unprecedented speeds and low costs. In particular, targeted sequencing of exomes has been extensively and successfully used to discover disease genes in Mendelian disorders or in cancer. However, with more than 30,000 variants found per exome, finding disease genes, even in cases of large and informative pedigrees, is a cumbersome, time-consuming task with a non-negligible artisanal component.
Most of the available tools cover the primary analysis (QC, alignment, and variant calling) that ends up in a list of variants found in sequencing experiments (VCF file) that can be annotated with different programs (ANNOVAR, VARIANT, VAAST, etc.) BiERapp fills the gap that leads from the properly annotated VCF file to the final candidate gene.
In the Tutorial you will learn how to use BierApp web application. Tutorial covers main functionalities such as:
- User interface functionality.
- BiERapp inputs and outputs.
- Filtering options.
- Creating an account.
To report an error or suggestion, please contact us at: babelomics@cipf.es