GATK's CNV-caller output, genotype code?

Question

[Joel Wallenius]

Hello!

I read the GATK docs and while they explain what their output contains, they don't explain what the content of their outputs mean. In my VCF outputs from PostprocessGermlineCNVCalls I have of course genotype, "GT", and it takes several values, apparently code like so:

0: expected (ref) copy number i.e. 2 for autosomal, 1 for male X/Y, 0 for female Y.
1: deletion
2: duplication

I learned this code from another Biostars post. But, then I have some GTs that are "./.", what is that supposed to mean? Missing? But why is it included in the output if it's missing?

Thanks in advance for your help and support, and have a merry weekend :)

Joel

Answer 1

[Rui Xu]

I am also new to this utility PostprocessGermlineCNVCalls, but hope my conjectures and understanding can be helpful to you.

I think you can combine the GT result with CN, which represents copy number.

For example, when CN equals to 0, 1, 2, you can easily detect the GT: CN=0 -> GT=1/1 (both deleted) CN=1 -> GT=0/1 (one deleted, one normal) CN=2 -> GT=0/0 (both normal) (you can check that in your own files when the ploidy is 2)

However, when the CN is above 2, you can't get the GT directly from the CN. For example, CN=3 -> maybe 2+1 in two chromatids, OR 3+0 CN=4 ......