Frontiers in Genetics (Sep 2021)

HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of Copy Number Variant, Copy Number Variation Region, and Runs of Homozygosity

  • Jinghang Zhou,
  • Jinghang Zhou,
  • Liyuan Liu,
  • Liyuan Liu,
  • Thomas J. Lopdell,
  • Dorian J. Garrick,
  • Yuangang Shi

DOI
https://doi.org/10.3389/fgene.2021.731355
Journal volume & issue
Vol. 12

Abstract

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Detection of CNVs (copy number variants) and ROH (runs of homozygosity) from SNP (single nucleotide polymorphism) genotyping data is often required in genomic studies. The post-analysis of CNV and ROH generally involves many steps, potentially across multiple computing platforms, which requires the researchers to be familiar with many different tools. In order to get around this problem and improve research efficiency, we present an R package that integrates the summarization, annotation, map conversion, comparison and visualization functions involved in studies of CNV and ROH. This one-stop post-analysis system is standardized, comprehensive, reproducible, timesaving, and user-friendly for researchers in humans and most diploid livestock species.

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