Journal
GENETICS
Volume 198, Issue 3, Pages 847-+Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.114.169052
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Funding
- National Science Foundation (NSF), a Cornell Center for Vertebrate Genomics Seed Grant [SGER DEB 0855879, DEB 1257628]
- Andrew W. Mellon Student Research Award
- Cornell Laboratory of Ornithology Athena Fund
- NSF Graduate Research Fellowship
- Cornell Center for Comparative and Population Genomics Fellowship
- Division Of Environmental Biology
- Direct For Biological Sciences [1257628] Funding Source: National Science Foundation
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Restriction site-associated DNA sequencing 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 a 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 GBS 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. These results demonstrate that our metric of Mendelian inheritance is a powerful quality filter for GBS loci that is complementary to standard coverage and HardyWeinberg filters. The described method, implemented in the software MendelChecker, will improve quality control during SNP discovery in nonmodel as well as model organisms.
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