Control-FREEC and Exome data, how to?

[Miau]

Hello everyone,

I am analysing some WES data in Control-Freec. However, there is a LOT of noise, and this noise is generating a lot of false positives when finding CNV regions.



My [general] config is similar to this, and while I consider it is quite restrictive, maybe I am wrong in something. Is there any problem with it?

[general]
BedGraphOutput = TRUE
chrLenFile = /home/...
contamination = 0.2
contaminationAdjustment=TRUE
maxThreads = 4
noisyData = True
outputDir = /....
ploidy = 2
printNA = TRUE
readCountThreshold = 50
sex = XY
chrFiles = /...
forceGCcontentNormalization = 2
minCNAlenght = 4
window= 500
breakPointType = 4
breakPointThreshold = 1.5
step = 250

I am sorry, but i am still learning to find CNVs with this, and I think with exomes everything is more complicated >.<


Thank you very, very much.