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Canvas - Copy number variant (CNV) calling from DNA sequencing data
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help to interpret CN value for calls with <DUP> alternative allele #124

Closed jazberna1 closed 5 years ago

jazberna1 commented 5 years ago

Hello,

I was wondering I you could please help me to interpret CN value for calls with alternative allele.

After running canvas I see vcf calls with as the alternative allele, all also having './1' genotype, which I understand means the reference allele (one copy on one chromosome) and then and elevated number of copies in the other chromosome (the ).

As the CN field gives the total copy number, can I assume that the number of duplications corresponding to equals to CN - 1 ?

Thanks so much Jorge

eroller commented 5 years ago

'./1' is different than '0/1' where 0 is the reference allele (i.e. one copy on chromosome A). The '.' means missing/unknown allele. So we do not know the copy number on chromosome A, but we know the copy number on chromsome B is > 1 (i.e. <DUP> for duplication).

You could imagine a complex CNV with overall copy number 3 that actually includes a deletion on chromosome A and 3 copies on chromosome B. Basically, in the case of GT='./1' Canvas is not identifying the per chromosome copy number, just the overall copy number listed in the CN field.

jazberna1 commented 5 years ago

Hello Eric,

Thanks so much! All is clear now. Jorge