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4.7 years ago
akhter.nisa
•
0
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?
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.