Estimating Genome-Wide Significance for Whole Genome Sequencing
Studies, Either Single SNP Tests or Region-Based Tests
Description
The correlations and linkage disequilibrium between tests can vary as a function of minor allele frequency thresholds used to filter variants, and also varies with different choices of test statistic for region-based tests. Appropriate genome-wide significance thresholds can be estimated empirically through permutation on only a small proportion of the whole genome.