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--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
--useBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --refFile)
--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
PhoneHome:
--noPhoneHome : disable PhoneHome (default enabled)
--noPhoneHome : disable PhoneHome (default enabled)
--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
