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

Jinghang Zhou; Liyuan Liu; Thomas J Lopdell; Dorian J Garrick; Yuangang Shi

doi:10.3389/fgene.2021.731355

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

Front Genet. 2021 Sep 17:12:731355. doi: 10.3389/fgene.2021.731355. eCollection 2021.

Authors

Jinghang Zhou^{1

2}, Liyuan Liu^{1

2}, Thomas J Lopdell³, Dorian J Garrick², Yuangang Shi¹

Affiliations

¹ School of Agriculture, Ningxia University, Yinchuan, China.
² AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand.
³ Research and Development, Livestock Improvement Corporation, Hamilton, New Zealand.

Abstract

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.

Keywords: CNVR; SNP; copy number variant; haplotype; run of homozygosity.

Associated data

figshare/10.6084/m9.figshare.3145759