Variant Impact tab

The legend at the top of the heat map is color-coded for the following variant impacts using the associated score values:

  • unknown: 0

  • synonymous: 1

  • missense: 2

  • non-frameshift block substitution: 3

  • non-frameshift insertion: 4

  • non-frameshift deletion: 4

  • nonsense: 5

  • stop-loss: 6

  • frameshift block substitution: 7

  • frameshift insertion: 7

  • frameshift deletion: 7

  • splice variant: 8

Set the Scoring menu to a different option, such as SIFT or PolyPhen2 , to base the legend and the heat map on those scores.

Clustering in Variant Impact heatmapFor variant impact heat maps, based on the scoring criteria selected from chart options, most deleterious score is picked for every gene-sample pair to generate the heat map. Thereafter hierarchical clustering is conducted for clustering genes and samples within the heat map.