Hi GATK Team,
I am using Mutect2 in mitochondrial mode on rat RNA-seq data (I don't have WGS data available).
It is not super clear to me if filtering NuMTs with the flag --autosomale-coverage of FilterMutectCalls also works with RNA-seq data, since the mtDNA has its own transcription initiation mechanism different from the nuclear one. Could you please help me with that ?
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