Tools

Tools developed in the Team

FrEx : The French Exome Project

The FREX project is a federative project that aims at building such a database and at giving access to the scientific community to exome data that can serve as controls in association studies. A total of 600 individuals sampled in 6 French regions have been sequenced using the Agilent V5+UTR exome capture kit and genotyped on Illumina Core Exome SNP-chip.

See FrEx

GEMPROT: GEnetic Mutation to Protein Translation

GEMPROT (Genetic Mutation to Protein Translation) is a tool to visualize the changes induced on the protein by the different variants found within a gene in an individual. Starting from a phased vcf, it translates the two haplotypes of each individual into the two corresponding protein sequences, allowing to vizualize if variants are in cis or trans.

See Gemprot

Ravages :

Ravages is an R package to perform rare variant association tests (RVAT) and genetic simulations

See Ravages

RavaQ :

An integrative pipeline for region-based rare variant association studies including quality control, qualifying variant selection and association tests

See RavaQ

VCFProcessor :

VCFProcessor is a tool to handle VCF File. In some points it is similar to vcftools and bcftools.

 

VCFReporter :

VCF Report is a tool that annotated a VCF File and builds a webpage report. The pages show the variants that are at least as severe as the selected VEP consequence. The report contains one page per selected gene and one page per sample in the VCF file.

See VCFReporter

PrivAS : Privacy-Preserving Association Studies

PrivAS is a tool to perform Genome-Wide Association studies (GWAS) using the Weighted-Sum Statistic (WSS) algorithm in a Privacy-Preserving environment. The underlying scenario takes into account three interacting parties:

  1. a Client, e.g. a genomic research unit, wanting to measure the association between an observed phenotype and regions of the genome
  2. a Reference Panel Provider (RPP) possessing genetic data for a Reference Panel, e.g. a priori healthy individuals of a carefully selected ancestry
  3. a Third-Party Server (TPS) with large computational capacities. 

Our tool and its underlying implementation preserve both state-of-the-art performances and Privacy for all parties. Indeed, through a series of hashing and encryption mechanisms, we can assure that no genetic data from neither the Client nor the RPP are visible by the other parties involved. Furthermore, only the Client is able to view a decrypted version of the WSS results.

See PrivAS

Ravages

Ravages was developped to simulate genetic data and to perform burden tests (a type of rare variant association tests) on more than two groups of individuals. Ravages relies on the package Gaston developped by Herve Perdry and Claire Dandine-Roulland. Most functions are written in C++ thanks to the packages Rcpp, RcppParallel and RcppEigen.
Functions of Ravages use bed.matrix to manipulate genetic data as in the package Gaston (see documentation of this package for more details).
In this vignette, we show how to simulate genetic data and we illustrate association tests using these simulated data. To learn more about all options of the functions, the reader is advised to look at the manual pages.

https://github.com/genostats/Ravages