Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference.

ABSTRACT: Single nucleotide polymorphisms (SNPs) in commercial arrays have often been discovered in a small number of samples from selected populations. This ascertainment skews patterns of nucleotide diversity and affects population genetic inferences. We propose a demographic inference pipeline that explicitly models the SNP discovery protocol in an Approximate Bayesian Computation (ABC) framework. We simulated genomic regions according to a demographic model incorporating parameters for the divergence of three well-characterized HapMap populations and recreated the SNP distribution of a commercial array by varying the number of haploid samples and the allele frequency cut-off in the given regions. We then calculated summary statistics obtained from both the ascertained and genomic data and inferr

SUBMITTER: Quinto-Cortes CD 

PROVIDER: S-EPMC6033855 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature