Comprehending Duplicates in Mutect2 and filtering

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Kate Newcomer

• August 20, 2024 20:53

Hi,

Looking for clarification. If a sam file goes through Picard's MarkDuplicates, but the duplicates are not removed does that impact variant calling in Mutect2?

 

Thanks,

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  Gökalp Çelik

  • August 22, 2024 19:37
  • Edited

  Hi Kate Newcomer

  Marked duplicates are filtered out by Mutect2 therefore they do not affect variant calling. In fact marking duplicates but not removing them is a better practice than removing them as the latter may result in loss of pairs. 

  Regards. 

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  Kate Newcomer

  • September 19, 2024 18:43

  Thanks!

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