Test-drive the GATK tools and Best Practices pipelines on Terra
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Disable duplicate read filter for M2
I have high coverage targeted sequencing data and would like to disable the duplicate read filter for Mutect2 (rather than skipping the de-duplication step in alignment).
Do I understand the documentation correctly that I should add the parameter
--disable-read-filter NotDuplicateReadFilter to the Mutect2 call? I would do this both for the tumor-only M2 (PON step) and paired M2 (calling step).