Mutect2 set variant filter in command line

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Hiral Desai

• November 02, 2022 20:23

I am using mutect2 for variant calling (The Genome Analysis Toolkit (GATK) v4.2.6.1). What command line option can be used to set variant frequency to 1% in mutect2 command line to decrease false positive results. Or is variant filtering based on frequency conducted after initial variant calling?

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  Anthony DiCi

  • November 07, 2022 18:55

  Thank you for your post, Hiral Desai! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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