Can you please provide
a) GATK version used 126.96.36.199
b) Exact GATK commands used Mutect2
c) The entire error log if applicable.
I am analyzing targeted sequencing data on tumor samples where I need to include PCR duplicates in the calling due to the probe design and I understand the filters below automatically applied to the data in Mutect2.
Is there a way to disable "NotDuplicateReadFilter" when running Mutect2?
These Read Filters are automatically applied to the data by the Engine before processing by Mutect2.
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