Genomic Diversity

This guide provides essential instructions for analyzing genomic diversity using the BIGapp. It walks users through the process of uploading and analyzing VCF files, selecting species ploidy, and interpreting results through various plots and tables. Additionally, it offers tips on saving images and files, as well as accessing in-app help and example files for a deeper understanding.

Alex Sandercock
12 steps
34 seconds

In the left hand side menu, select "genomic diversity".

Genomic diversity option highlighted in the main BIGapp left hand menu

Choose your VCF.

Choose VCF file input section highlighted

Once you have selected your file, click "open".

VCF file highlighted amongst other file options

Select the species ploidy.

Select "run analysis".

You can view your results in the middle of your screen. Note the various plot and table options.

Dosage plot tab option highlighted. Other options include MAP plot, HEP plot and others

The yellow informational button contains a file example, links to in-app help documents and the option to view the summary metrics.

Options under informational tab including example files, parameters, results, citation and summary

Move through the various plots and tables by clicking on the tab with the corresponding name. Notice that you have access to plot controls on the left hand side of the graphic.

Histogram bins plot controls highlighted

Ohet Plot example

OHet plot tab highlighted and OHet plot shown

Marker plot example

Marker Plot tab higlighted and marker plot shown

You can also view additional information about the mean heterozygosity and mean MAF across all samples on the upper right-hand side of the screen.

Mean heterozygosity informational section highlighted

Use the red button on the left hand side under plot controls to save. \ Make your various figure selections. When you are satisfied you can save the image as well as the file by clicking on the grey boxes at the bottom.

Save image and save file options highlighted and optional menu open

You have completed this training module for Genomic Diversity in the BIGapp. Return to the main training page to learn more about other BIGapp features.