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Filter in DepthOfCoverage 3.3-0
We've been using the DepthOfCoverage tool in our pipeline and noticed that the =>Q30 score per gene provided by GATK is significantly different than the =>Q30 score we calculate ourselves without any filters. On your manual page for DOC, you mention using several filters (although it isn't specified if this applies to all versions of GATK or just the last one):
In your general manual page, you mention there is a parameter for disabling filter (--disable_read_filter, -drf). This doesn't seem to be implemented yet in 3.3-0, seeing as I get an error that the argument isn't defined and the argument isn't showing up in the help page either. Is there another way to disable filters in 3.3-0?