An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

ABSTRACT: Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage geno

SUBMITTER: Benjelloun B 

PROVIDER: S-EPMC7115901 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature