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Germline CNV, the correct order of using the involved tools.

Dear all,

I know that the tutorial is not available yet for the Germline CNV and it is still in beta, but can anyone just write some numbered points about the order of the involved tools please? just as points. To my understanding it is something like this:
1- CollectReadCounts
2- DetermineGermlineContigPloidy
3- GermlineCNVCaller
4- post processing to get the vcf file

Are those steps enough to be considered? Or are there any extra beneficial steps that might be added in between?

Many thanks for the help

Best Answer


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