To use the Variant Comparison Tool Top List function
You
use the Top List function to analyze somatic variants that can be found in a mutant sample/normal sample comparison, or in a multiple sample similarity comparison. In a mutant sample/normal sample comparison, such as a tumor/normal comparison, you can load only two sample project files—the mutant sample project file and the normal sample project file. The Top List function ranks the detected variants in these two files and returns the top 100 results for the following three types of variants:
• Gain in heterozygosity variants, which are low frequency novel/somatic variants in the normal sample.
• Loss of heterozygosity variants, which are low frequency variants in the mutant sample.
• Absolute change variants, which are the variants with the most significant allele change and that are not low frequency in either the mutant sample or the normal sample.
In a multiple sample similarity comparison, you can load up to 20 sample project files. The Top List function returns a list of variants that have the highest rankings in all the files. The variants’ rankings are based on the three criteria—the number of samples that share the variant, the frequency at which the variant occurs in each sample, and the size of the standard deviation for the allele frequency between samples.