Mutect2 filter : clustered_events definition

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whynot

• February 12, 2020 05:08

Hi. I'm student who study bioinformatics.

I make some vcf files using GATK3.6 tumor only mode.

 

I wonder about 'clustered_events' filter's definition.

According to the vcf meta-information line, 

##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">

And I got the information that 'clustered event' is several mutations that are close together.

What is the criteria about 'close together'?

How close does it take to be perceived as 'clustered'?

 

please answer about this, thanks!

 

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  David Benjamin

  • February 12, 2020 05:21

  "Clustered" mean co-occurring in the same local assembly interval, usually about 200bp.  By the way, you should upgrade to the most recent release of GATK 4.  The GATK 3 version of Mutect2 is obsolete.

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  whynot

  • February 12, 2020 06:55

  Thanks for answer!

   

  Can I have one more question?

   

  I got new information about clustered_events filter.

  When they count 'clustered' variants, they have another condition:

  "variants with distance between >= 3 bp"

  The reason I thought this condition was true is that if the distance between variants in my vcf file is less than 3 bp, I did not get caught by the clustered_events filter.

  Is that really right condition?

  If that's right, then "clustered" mean co-occurring in the same local assembly interval, about 3-200bp?

   

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  David Benjamin

  • February 12, 2020 15:57

  I think the intent was to avoid filtering MNPs.  We do it differently in GATK 4.  I can't emphasize enough how important it is to upgrade to the most recent GATK 4 version.

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  Dario

  • May 16, 2020 00:30

  Is there a table of filters containing detailed definitions of all of the possible ones in a document somewhere? The VCF header ones are too short for readers who weren't involved with the development of the software.

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  David Benjamin

  • May 17, 2020 01:06

  The most current Mutect2 documentation can be found in our github repo here: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf

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  Дмитрий Голик

  • August 30, 2022 14:02

  David Benjamin unfortunately there is not description for every possible filtering outcome.

  And how i should handle MNPs in GATK 4?

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  David Benjamin

  • September 12, 2022 16:10

  Привет, Дмитрий, есть конкретная ситуация, которая тебя интересует?

  Что касается MNPs, используйте опцию `--max-mnp-distance`.  Когда это Ноль, GATK считает их независимыми SNPs.

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