countsN meaning & example

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Mingzhou Fu

• September 08, 2021 15:38

Hi there,

I'm using gatk variantannotator to add some extra annotation to my vcf file, and got somehow unclear about the 'CountNs'. I've checked the doc https://gatk.broadinstitute.org/hc/en-us/articles/4404607611931-CountNs, but still could not think of a real world example. Does the N means any A,T,C,G? could you please provide a toy example? 

Thank you!

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  Genevieve Brandt (she/her)

  • September 08, 2021 20:32

  Hi Mingzhou Fu,

  There is more information in the github release of that annotation, though not much: https://github.com/broadinstitute/gatk/pull/5317

  It's not a common annotation for general usage as far as I know. The developers who have worked on this annotation primarily work on Mutect2 and it also looks like the planned liquid biopsy pipeline. N's are not any particular nucleotide, they represent gaps in the genome. Here are some links:

  • https://www.biostars.org/p/67068/
  • https://www.biostars.org/p/227632/

  Hope this helps!

  Genevieve

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  Mingzhou Fu

  • September 08, 2021 22:25

  Got it! Thank you for the links! Now I understand this annotation. 

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