Aphelocoma coerulescens SNP discovery

Genotyping-by-sequencing data and custom Illumina iSelect Beadchip genotypes for the Florida Scrub-Jay. Data associated with: Chen N, Van Hout CV, Gottipati S, Clark AG. 2014. Using Mendelian inheritance to improve high throughput SNP discovery. Restriction-site associated DNA sequencing (RAD-seq) or genotyping-by-sequencing (GBS) approaches allow for rapid and cost-effective discovery and genotyping of thousands of single nucleotide polymorphisms (SNPs) in multiple individuals. However, rigorous quality control practices are needed to avoid high levels of error and bias with these reduced representation methods. We developed the first formal statistical framework for filtering spurious loci using Mendelian inheritance patterns in nuclear families that accommodates variable-quality genotype calls and missing data – both rampant issues with RAD-seq data – and for identifying sex-linked SNPs. Simulations predict excellent performance of both the Mendelian filter and the sex-linkage assignment under a variety of conditions. We further evaluate our method by applying it to real GBS data and validating a subset of high quality SNPs. Our results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for RAD-seq/GBS loci that is complementary to standard coverage and Hardy-Weinberg filters. The described method, implemented in the C++ software MendelChecker, will improve quality control during SNP discovery in non-model as well as model organisms.