Mutect2 --enable_clustered_read_position_filter not available in GATK4
Currently trying to update a script from GATK 3.8 to 4, and using the tool Mutect2.
It seems that some of the parameters have been excluded in the process. I am trying to find a similar parameter to --enable_clustered_read_position_filter in GATK 4, but no avail so far. Any possible suggestions?
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Have you tried posting on GATK forums? They updated the somatic calling when they went from GATK3 to GATK4 so they might not have a parameter similar to the one you mentioned.