I'm using GATK 4.3.0.
I was wanting to create my own PON for CNV analysis. I have no matched normals and I'm using a different sequencing technology to Illumina.
I was wondering if it was possible for me to use some freely available GIAB (i.e. NA12878 - sequenced with the same technology) to create the PON. I think I will only have two maybe three available to me to create the PON.
I know you would recommend a minimum of ~ 40 samples but is do you think I could still get useable information from this?
And just to check, can you do CNV analysis if you have tumour only by using this PON?
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