Orientation bias filter on germline analysis

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Alexandre Defelicibus

• June 23, 2021 19:00

Hi all,

How can I use the orientation bias filter on germline variant analysis (if it is possible)?

Best,

Alexandre

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  Pamela Bretscher

  • June 24, 2021 14:05

  Hi Alexandre,

  
  I am going to move your post into our Community Discussions -> General Discussion topic, as the germline topic is for reporting bugs and issues with GATK.
  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,
  Pamela

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  Genevieve Brandt (she/her)

  • July 13, 2021 23:36

  Hi Alexandre Defelicibus,

  I think the orientation bias filter you are thinking of is part of FilterMutectCalls, which only works for somatic data. We wouldn't recommend you try this with germline data. 

  The filtering methods for germline data are CNN, VQSR, and hard filtering. You can read more about these methods at the following links and choose the right filtering method for your analysis:

  • https://gatk.broadinstitute.org/hc/en-us/articles/360056969932-CNNScoreVariants
  • https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering

  Hope this helps! Please let me know if I misunderstood what you are looking for.

  Best,

  Genevieve

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