Is it possible to report the allele frequency of integer copy numbers >= 3?
I am using cn.mops which reports integer CNV for samples (eg CN1, CN3, CN4, CN5, etc.)
I hope to report haplotype frequency of detected CNVs, but I am struggling to understand if this is possible.
If CN1, seems straightforward because they have one copy of the CNV across both haplotypes. So if 50 of 100 people have CN1 of some CNV, the allele frequency should be: 50/200 = .25
But if reported CN4, this could be one haplotype CN3 and the other CN1 or both haplotypes CN2, etc.
With these data is it even possible to report haplotype frequency of CNVs for cases other CN1? If so how would I proceed?
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