Why Are Sample Statistics Not Automatically Updated in GenomeStudio v2.0 After SNP Clustering or Cluster Modifications?

During GenomeStudio Genotyping Module project creation, SNP data can be clustered by applying a user-selected cluster file or by using the built-in clustering capabilities of GenomeStudio to generate clusters from the sample data. After clustering is complete, the option to calculate SNP statistics is available.

Figure 1. Calculate Sample and SNP Statistics button in the Project Wizard.

Upon completion of the calculations, all sample statistics in theSamples Table, including call rates, are generated and displayed.

If subsequent changes are made to SNP clustering, such as applying an alternative cluster file or manually adjusting the clustering of one or more SNP assays, the statistics in the Samples Table are not automatically recalculated.

Instead, several of the data columns in the Samples Table are highlighted in red to indicate that the statistics are no longer current. In addition, a Calculator button appears at the far right of theSamples Table toolbar, indicating that the statistics can be recalculated.

Figure 2. Calculator icon in the Samples Table used to manually recalculate sample statistics after SNP clustering changes.

Users may wonder why these statistics are not automatically updated after each clustering change. The reason is that recalculating sample statistics can be a time-consuming process, particularly in projects containing a large number of samples.

During SNP review and cluster refinement, such as when evaluating the results of a Cluster All SNPs operation, users may make numerous clustering adjustments. Automatically recalculating the Samples Table statistics after every individual change could significantly impact performance and prolong the review process.

GenomeStudio does not automatically update the statistics following clustering modifications. Instead, the software highlights the affected statistical columns in red, displays a Calculator button in the Samples Table toolbar, and allows users to continue making clustering changes as needed before initiating a single recalculation of the statistics. This approach enables all modifications to be processed together rather than recalculating the statistics after each individual change.

Upon completion of the recalculation of SNP Table statistics, the statistical columns return to their normal background color and the Calculator button disappears until new clustering modifications are made within the project.

Reference:

GenomeStudio Genotyping Module v2.0 User Guide

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