My GitHub repository : https://github.com/cbherer
CERC team repository : https://github.com/CERC-Genomic-Medicine/
Sex-specific Genetic Maps
The female, male and sex-averaged genetic maps described in Bhérer et al. 2017 Nature Comms are available here. These high-resolution recombination maps were build using data derived from 3.3 million crossovers from over 100,000 meioses. My Github repository contains the different maps described in the paper (Refined, European, DeCODE2014), and the code to interpolate recombination rates in bins of arbitrary size. The posterior estimates of recombination rates were obtained using our MCMC method (rMCMC).
rMCMC – A Gibbs sampler to build high resolution recombination maps
This is a MCMC method to improve the resolution of recombination rates estimates using pedigree-based data. The idea is to combine crossover information across multiple families to refine the localization of recombination events, therefore allowing to estimate recombination rates at a finer scale. For details on the method and algorithm see Bhérer et al. 2017 Nature Comms. Download code from here.
Phenoselect – A 3-population test for selection on polygenic phenotypes
This is a method to detect polygenic adaptation in a three-population tree. The method was described at the Biology of Genomes meeting (Poster) and the Probabilistic Modeling in Genomics meeting (talk) in Aarhus, Denmark, in 2017. Download code from here.
The Quebec Reference Sample
The Quebec Reference Sample is a data resource for studies in genetic epidemiology and population genomics in Quebec, now hosted at BALSAC. We recruited volunteers whose grand-parents were born in specific regions of Quebec and consent to give genetic and demographic information. DNA analysis were performed in Labuda’s group at CHU Sainte-Justine research center, and genealogies were build using the BALSAC database. The anonymized genomic and genealogical data from a subset of participants is available upon request, as described in Roy-Gagnon et al. 2011 and Moreau et al. 2013.