germlineCNVCaller Procedure

Hello,

I am trying to use the gCNV caller to call CNVs in a large set of samples. I am trying to figure out how to do so, but am quite confused as to the proper steps to take, and inputs and outputs for each step.

Are you to run DetermineGermlineContigPloidy-cohort and than DetermineGermlineContigPloidy-case mode? then use that model for germlineCNVcaller-cohort and then proceed to germlineCNVcaller-case?

or are you to run DetermineGermlineContigPloidy-cohort, then germlineCNVcaller-cohort, DetermineGermlineContigPloidy-case , germlineCNVcaller-case?

Can someone clarify the order of the steps one is to take to follow the proper best practices?