If I call HaplotypeCaller with
--help
it says that with -drf I can name "read filters to disable". Notice the plural. So I assume disabling multiple filters must be possible somehow. I'm trying to find out how to pass multiple filter names since there seems to be no documentation about this.
Using
-drf HCMappingQuality DuplicateRead
results in an error but more importantly
-drf HCMappingQuality -drf DuplicateRead
results in a java.lang.IllegalStateException
I think the latter is a bug and besides: How to pass multiple filter names to the -drf option? 