Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies.

Identification of variant-level differences in genotype quality and alternative allele fraction between two exome capture kits As the PCA plot of the 29 novel SNPs showed significant batch differences of genotypes between samples processed by two exome capture kits, we next examined variant-level factors that could explain why exclusively the Illumina kit-captured exomes yielded this set of highly significant novel SNPs.

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