Chunk #36 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Using detected recombinations for association scans of hotspot usage
The accuracy with which is measured increases with the number of crossovers observed for that parent, hence parents with more observed crossovers should be given higher weighting (large nuclear families are advantageous in this situation). We weighted individuals by creating pseudo-counts of hotspot events where is the number of crossover events observed for parent . We then fit a standard Binomial Generalised Linear Model (GLM) with as the response and the genetic dosage at each SNP as the covariate. We then performed a likelihood ratio test between this model of association and the ‘null’ model where no genetic variant is included. Variants were imputed from the 1000 Genomes March 2012 reference panel and filtered such that all variants had and in all cohorts.
