lantern - Ancestry-Specific Rare Variant Association Analysis

Ancestry-specific rare variant burden testing for admixed populations. Splits genotype dosages by local ancestry (as inferred by 'RFMix') into per-ancestry dosages, using either phased haplotypes or unphased genotypes with shrinkage toward global ancestry, and writes them to 'SeqArray' GDS files. Ancestry-stratified gene-level tests are then run with the 'SMMAT' framework of Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012> as implemented in 'GMMAT', and the per-ancestry p-values are combined with the Cauchy combination test of Liu and Xie (2020) <doi:10.1080/01621459.2018.1554485>.