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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal
Nathan A Kinsey1, Janelle M Belanger1,
1Department of Animal Science, University of California, Davis, USA.
Abstract:
Deficient homozygosity of a variant maintained in a population suggests that the variant may be embryonic lethal. We examined whole genome sequence data from 675 canids to investigate for variants with missing homozygosity and high predicted impact. Our analysis identified 45 variants, in 32 genes. However, further scrutiny of the sequence reads revealed that all but one of these variants were artifacts of the variant calling process when using CanFam3.1, a widely utilized canine reference genome. We demonstrate that the use of multiple, newer reference genomes could reduce artifacts and lead to more accurate variant identification.
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