Dr

[lkadalayil]

II am interested in tumour-specific exome CNVs and am using VarScan2. I have finished a preliminary analysis but am stuck with the interpretation.

The output after CBS gives a variable called num.mark.

• What does marker mean here?
• Does it have any relationship to the baits in the capture kit? But then VarScan or CBS never asked for any bed files.
• Alternatively, is CBS comparing with a reference and detecting alternate alleles/SNPs and calling them as markers?

Any comments will be appreciated

[Richard Finney]

the number of probes on the array that are represented in the region

[lkadalayil]

I am sorry, what is the definition of a probe then? I am a molecular biologist turned statistician. In my dictionary a probe is an oligonucleotide used to hybridise with a piece of DNA to be PCRed or sequenced. How does VarScan/CBS know which such probe was used? It didn't ask for a bed file containing that information.