A quick question; if I want to calculate the AF based on deletions and duplications, which one do I take into account for the calculation?
For example, I need to have the number of homozygous deletions or duplications to do the calculation but I could not find anywhere which copy number variant we need. Is it based on what CNVs take the majority on that specific gene or chromosome?
Thank you for your response Jorge. I have done exactly what you said. I have calculated how frequent each number of copies are. My question was whether I calculate the AF according to the copy numbers which represent the deletions or the copy numbers which represent the duplications.
when dealing with copy number variation you know which is the motif and the number of times that it's repeated. the number of times the motif is repeated is what you would consider an allele.
say you have 6 copies on the reference, and on different samples you have 5, 5, 5, 5, 5, 6, 6, 7, 7, 7 copies. then the 5 copies would have a 0.5 AF, the 6 copies would have a 0.20 AF, and the 7 copies would have a 0.30 AF.