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ABSTRACT. Quality control filtering of single nucleotide polymorphisms (SNP) is a key step when analyzing genomic data. Here, we present a practical method to identify poorly genotyped SNPs by detecting those for which gene content deviates from the pedigree-based expectation. This can be achieved by estimating the heritability of gene content at each marker, defined as the number of copies of a particular reference allele in a genotype of an animal (0, 1 or 2). The method uses Restricted Maximum Likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood ratio test statistic to test for zero error variance in genotyping. The proposed method is illustrated with a real dataset with genotypes from Illumina PorcineSNP60 chip.

FORNERIS, N. S. , LEGARRA, A. , VITEZICA, Z. G. , TSURUTA, S. , AGUILAR, I. , CANTET, R.J.C. , MISZTAL, I.
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In:Proceedings of the World Congress on Genetics Applied to Livestock Production, 10., Vancouver, BC, Canada, August 17-22, 2014. p.471.
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