disabling NotDuplicateReadFilter in Mutect2
Can you please provide
a) GATK version used 4.1.4.1
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?
Thanks!
Read filters
These Read Filters are automatically applied to the data by the Engine before processing by Mutect2.
- NonChimericOriginalAlignmentReadFilter
- NotSecondaryAlignmentReadFilter
- GoodCigarReadFilter
- NonZeroReferenceLengthAlignmentReadFilter
- PassesVendorQualityCheckReadFilter
- ReadLengthReadFilter
- MappedReadFilter
- MappingQualityAvailableReadFilter
- NotDuplicateReadFilter
- MappingQualityReadFilter
- MappingQualityNotZeroReadFilter
- WellformedReadFilter
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Hi ,
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Hi jungmin choi,
There are arguments that you can apply with Mutect2 (and other GATK tools) to either disable specific read filters (--disable-read-filter) or all default read filters (--disable-tool-default-read-filters). Further information can be found on the Mutect2 documentation page.
I hope this is helpful.
Kind regards.
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