SABER

SABER is a program suitable for genome-scale data which uses a “Markov-hidden Markov model” to estimate local ancestry (Tang H, Coram M, Wang P, Zhu X, Risch NJ. (2006) Reconstructing Genetic Ancestry Blocks in Admixed Individuals. Am J Hum Genet. 79:1-12.). This local ancestry is referred to as “ancestral blocks”. Like HAPMIX, it models the ancestral LD; however it does not model haplotype structure. Input files are typical and include genotype data from ancestral and admixed individuals, global ancestry estimates of admixed individuals, and physical map location of the SNPs. In addition to providing localized ancestry (with graphical output), SABER can be used to estimate time since admixture. Reconstructing Genetic Ancestry Blocks in Admixed Individuals