Mutect2: NuMTs filtering on RNA-seq
AnsweredHi 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 ?
Thanks !
Léore
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This should work, provided that you interpret autosomal coverage correctly. The autosomal coverage represents the average coverage of the autosome in the BAM. For RNA, it would represent how much autosomal RNA is in your BAM. So, the value might be different with RNA seq but it won't change your ability to use the flag.
Best,
Genevieve
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