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Statistical Detection of Genome Differences Based on CNV Segments

  • Yang Zhou
  • Derek M. Bickhart
  • George E. Liu
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)

Abstract

Population analysis using copy number variation (CNV) is far more complex than analysis using SNPs because of the diverse copy number and inconsistent boundaries of CNVs in different individuals that causes changes in frequency. Multiple studies have reported CNV regions associated with diseases or body traits based on a CNV segmentation strategy that condenses calls from multiple different sources into a genotype state. Here, we provide a guideline of how to generate CNV segments from known CNV results, and how to detect genome differences based on CNV segments.

Key words

CNV segments PennCNV FST Lineage differences Misassemblies 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Yang Zhou
    • 1
  • Derek M. Bickhart
    • 2
  • George E. Liu
    • 3
  1. 1.Huazhong Agricultural UniversityWuhanChina
  2. 2.Research Microbiologist/BioinformaticianUSDA ARS DFRCMadisonUSA
  3. 3.Animal Genomics and Improvement LaboratoryUSDA ARSBeltsvilleUSA

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