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--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
--useEquals : Convert any bases that match the reference to '=' (requires --refFile)
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<pre> PhoneHome:
--noPhoneHome : disable PhoneHome (default disabled)
--phoneHomeThinning : adjust the PhoneHome thinning parameter (default 50)
Optional Parameters:
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{{InBAMInputFile}}
{{InBAMInputFile}}
{{OutBAMOutputFile}}
{{OutBAMOutputFile}}
