ClusterPlot viewer V3C

V3C is a graphical tool in Sandbox used for:

• improving the automatic calls of rare variants

• looking at batch variation

V3C runs on a text file that contains intensity values for many individuals in FinnGen. This individual-level intensity data is available only in Sandbox (in contrast to the cluster plot image files which can be downloaded from the green library). For instructions on locating the intensity file please see the section Rare Variant Calling in V3C.

ClusterPlot viewer V3C in Genotype Browser

From Sandbox v10.3 onwards the Cluster Plots viewer V3C tool is also provided within Genotype Browser's Interactive Filters view. For more information on Cluster Plots and where to find cluster plots made from FinnGen data see the Cluster Plots chapter.

Install ClusterPlot viewer V3C

You can also use V3C on a separate browser page in Sandbox IVM. To install it:

(After the initial installation, you can in future skip steps 1 and 2 to run the viewer.)

1. Copy the zip archive to your IVM: cp /finngen/shared/v3c/20220403_122900/files/mpreeve/V3C_01042022.tar /home/ivm

2. tar cvf V3C_01042022.tar

3. cd FinnGen-Cluster-Plot

4. firefox finngen_plot.html