Calculating Concordance In Illumina's Genome Studio 2.0

Concordance is an agreement between two datasets. To calculate this important data science and bioinformatics metric in Genome Studio 2.0, the steps are simple but not always intuitive and (new) user-friendly.

To begin, two Genotyping projects would have already been analyzed and are ready for a Concordance analysis. An experiment on two projects would be such as, for example, a before and after validation on equipment before and after a move and etc. The Sample Names from the Sample Sheet for both Project A and Project B must have the same names so they can be pairwise compared correctly.

Go to Project A in Genome Studio 2.0. Under "Analysis" -> "Export Allele Calls" -> Choose "Top/Bottom Strand" (only; we were notified of and participated in recognizing a software bug in Genome Studio 2.0 that relates to incorrect Concordance values when choosing "Plus/Minus Strand" when compared to our in-house Concordance script output). Save these files in a folder that is descriptive, something like "Project-A_Top-Bottom-Strand_Allele-Calls_{Your_Initials}_{Day-Month-Year}."

Either close the project or open another Genome Studio 2.0 window and open Project B. Under "Analysis" -> "Import Allele Calls" -> Browse for the folder and Choose "Top/Bottom Strand".

What happens next is nothing unless the following extra steps are taken.

Under the "Samples Table" -> "Column Chooser" -> "Displayed Subcolumns" -> "Concordance." The values are red and NaN by default, which can be confusing. In order to calculate the values, on the far left of the Samples Table icons, click on the new calculator icon. Concordance values can now be calculated and should be viewable.

Under the "Full Data Table" -> "Column Chooser" -> "Displayed Subcolumns" -> choose "Top Alleles," "Import Calls" and again, "Concordance." The calls that are concordant are equal to "1" and otherwise are "-1" which includes the case of no calls.

The best way to move forward with this information in Genome Studio 2.0 is to:

1. Export the Sample Table which has the Concordance values unrounded.
2. Save the project.

Illumina's Support Team are very knowledgeable and are generously helpful and have helped me in a previous Bioinformatician position in which I also have had to use Genome Studio. My appreciation goes out as well to screen sharing which is a phenomenal tool for troubleshooting.