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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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GCViT: a method for interactive, genome-wide visualization of resequencing and SNP array data.

Andrew P Wilkey1, Anne V Brown2, Steven B Cannon2

  • 1ORISE Fellow, USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA.

BMC Genomics
|November 24, 2020
PubMed
Summary

GCViT (Genotype Comparison Visualization Tool) aids in exploring large genotyping datasets, identifying genomic regions and relationships. This tool visualizes single nucleotide polymorphism (SNP) data for detailed analysis and discovery.

Keywords:
CViTGCViTGenotypeResequencingSNPUIVisualizationWeb service

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Efficient SNP identification methods generate large genotyping datasets.
  • Exploring these datasets requires tools for assessing accession differences and genomic anomalies.
  • Thousands to millions of data points exist across thousands of accessions.

Purpose of the Study:

  • To present GCViT (Genotype Comparison Visualization Tool) for visualizing and exploring large genotyping datasets.
  • To enable identification of introgressions, conserved/divergent regions, and pedigrees.
  • To facilitate whole genome visualization of resequencing or SNP array data.

Main Methods:

  • GCViT compares variants among user-selected accessions against a reference.
  • It identifies allele differences and similarities.
  • Visualizations are provided through histogram, heatmap, or haplotype views.

Main Results:

  • GCViT facilitates interactive, whole-genome scale visualization of SNP data.
  • The tool can identify introgressions, conserved/divergent regions, and pedigrees.
  • Analyses and images generated by GCViT are exportable in various formats.

Conclusions:

  • GCViT offers methods for interactive SNP data visualization on a whole genome scale.
  • It produces publication-ready figures and aids in identifying genomics regions of interest.
  • GCViT is available online and as a local installation.