A pipeline was developed to determine local ancestry in subjects with African and/or Native American admixture (AFA, AMA; Supplementary Fig. 28). Additional QC to consistently prepare cohort data for downstream analysis was performed with a custom script (https://github.com/eatkinson/Post-QC). Post-QC steps involved extracting autosomal data, removing duplicate loci, updating SNP IDs to dbSNP 144, orienting data to the 1KGP reference (with removal of indels and loci that either were not found in 1KGP or that had different coding alleles), flipping alleles that were on the wrong strand, and removing ambiguous SNPs.
