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Using MuTect for targeted DNA sequencing of miRNAs?

nroaknroak HoustonMember ✭✭

I have patient-normal dataset for targeted sequencing of known miRNAs.
I wanted to know if it is best to use MuTect pipeline to call for variants or independently use GATK on samples and make somatic calls.
The question roots from whether MuTect discards mutations from non-coding sequences at any step of analysis?

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  • nroaknroak HoustonMember ✭✭

    Thanks Kristian for the reply. Is there a way to get around by using data for miRNAs that are covered by exome capture? To my understanding, most exome captures cover ~700-800 miRNAs in the chip.

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