Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. The study compared genetic diversity measures estimated from individual genotyped array data with those estimated from pool whole genome resequencing data. Different different filtering options were applied to the array data to assess their potential to mitigate the ascertainment bias.