Project

GCViT: Whole genome visualization of SNP data

Goal: A whole genome visualization tool to display genomic features. GCViT can be used to compare sequence similarity between two or more genotyped accessions (either by re-sequencing or SNPchip). GCViT will plot differences and/or similarities between two or more accessions within a dataset using a VCF file. Similarity means that the same allele is present at the SNP position between the lines, difference indicates a different allele at the SNP position.

Date: 31 January 2019

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Project log

Anne V Brown
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Background Large genotyping datasets have become commonplace due to efficient, cheap methods for SNP identification. Typical genotyping datasets may have thousands to millions of data points per accession, across tens to thousands of accessions. There is a need for tools to help rapidly explore such datasets, to assess characteristics such as overall differences between accessions and regional anomalies across the genome. Results We present GCViT (Genotype Comparison Visualization Tool), for visualizing and exploring large genotyping datasets. GCViT can be used to identify introgressions, conserved or divergent genomic regions, pedigrees, and other features for more detailed exploration. The program can be used online or as a local instance for whole genome visualization of resequencing or SNP array data. The program performs comparisons of variants among user-selected accessions to identify allele differences and similarities between accessions and a user-selected reference, providing visualizations through histogram, heatmap, or haplotype views. The resulting analyses and images can be exported in various formats. Conclusions GCViT provides methods for interactively visualizing SNP data on a whole genome scale, and can produce publication-ready figures. It can be used in online or local installations. GCViT enables users to confirm or identify genomics regions of interest associated with particular traits. GCViT is freely available at https://github.com/LegumeFederation/gcvit. The 1.0 version described here is available at https://doi.org/10.5281/zenodo.4008713.
Anne V Brown
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Anne V Brown
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Tutorial for GCViT can be found here: https://youtu.be/B2gPVUipWo0
 
Anne V Brown
added a research item
GCViT is a tool to visually compare differences between two or more accessions in a dataset based on SNP data. Here is the GCViT front page found at soybase.org/gcvit
Anne V Brown
added an update
GCViT is now available on SoyBase at https://soybase.org/gcvit and Legume Information under Genome Wide Comparison of Genetic Variants (SNPs) at https://legumeinfo.org/germplasm.
 
Anne V Brown
added a research item
This picture shows the comparison of 15 soybeans lines, using the histogram and heatmap displays, to a wild G.soja soybean accession.
Anne V Brown
added an update
GCViT currently extracts data from a VCF and will plot where 2 or more accessions are the same or different on the chromosomes.
 
Anne V Brown
added a project goal
A whole genome visualization tool to display genomic features. GCViT can be used to compare sequence similarity between two or more genotyped accessions (either by re-sequencing or SNPchip). GCViT will plot differences and/or similarities between two or more accessions within a dataset using a VCF file. Similarity means that the same allele is present at the SNP position between the lines, difference indicates a different allele at the SNP position.