I was running ExomeDepth using my exome paired data with normal and tumor respectively.
While running ExomeDepth, I am not sure this tool is focused on detecting somatic copy number variation.
Just looking at its manual and I found "Load an example dataset" section as shown in below.
there are reference argument which user have to input.
test <- new('ExomeDepth',
+ test = ExomeCount.dafr$Exome2,
+ reference = ExomeCount.dafr$Exome3,
+ formula = 'cbind(test, reference) ~ 1',
+ subset.for.speed = seq(1, nrow(ExomeCount.dafr), 100))
Is it right that I should put my normal exome data as reference argument?
If not, Is there any method to detect normal and tumor comparison simultaneously (also known as somatic) using ExomeDepth?
It would be also great if you give me more information about your own process in detecting CNVs using ExomeDepth.