genotype files (.ped/.map) Local ancestry information: PCAdmix outputsfiles (.bed/.marker/.vit) per chromosome admixturemapping_pcadmix2additive012_African.r admixturemapping_pcadmix2additive012_European.r admixturemapping_pcadmix2additive012_NativeAmerican.r .ped/.map files with local ancestry (--recode12 format) per chromosome per ancestry .window file PLINK (--merge function) .ped/.map files for all autosomes per ancestry PLINK (--recodeA function) .raw files per ancestry phenotype information file (--pheno) covariates information file (--covar) PLINK logistic (--logistic function) or linear (--linear function) regression per ancestry linear or logistic regression outputs of PCAdmix windows Logistic or Linear Regression by R Scripts per ancestry Family cluster information file (for Bambui) Imputation and Fine mapping for each associated window Association Study for imputaded SNPs of each associated window Associated SNPs list SNP annotation Effective number of tests (ENT) estimation for each chr for each individual per ancestry: coda package ENT for each chromosome for each individual per ancestry ENT sum for all chromosome for each individual per ancestry ENT per individual per ancestry Calculation of ENT average across individuals per ancestry ENT average per ancestry Bonferroni correction: 0.05/ENT_average p-value threshold for significance per ancestry linear or logistic regression outputs of RFMix windows .raw files per ancestry of PCAdmix windows p-value threshold * 5 filtered PCAdmix windows filtered RFMix windows compare Windows Windows are mapped for the same regions? Windows excluded Consensus windows 2 Definition of p-value threshold Phenotype associated to a specific ancestry Admixed Population genetic data PCAdmix and RFMix: Local Ancestry Inference Parental Populations Genetic Data ADMIXTURE Individual Ancestry Inference No Yes