Panel of Normals containing somatic mutation due to tumour in normal contamination

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Shashwat Sahay

• September 19, 2024 21:45

Is there a way to filter out mutations in PON which are caused due to tumor in normal contamination?

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  Gökalp Çelik

  • September 19, 2024 22:41

  Hi Shashwat Sahay

  Are you using the PoN we provided or a PoN that you generated?

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  Shashwat Sahay

  • September 20, 2024 08:10

  Hi Gökalp Çelik,

   

  I am using the PoN created from 118 normals that we seqeuenced in a paired tumor normal strategy as our experiment is that of targeted panel sequencing. 

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  Gökalp Çelik

  • September 21, 2024 10:01

  Hi again. 

  Do you mean that you still want to call those mutations even if they are in PoN due to contamination?

  If that's the case you may force call those alleles by using the parameter 

  --genotype-pon-sites <Boolean>Call sites in the PoN even though they will ultimately be filtered.  Default value: false.
                                Possible values: {true, false}

  Those sites will still have non-passing filter however they will be visible in the VCF file and if you know which ones are those you can easily re-filter them in. 

  I hope this helps.

  Regards

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  Gökalp Çelik

  • September 23, 2024 17:47

  Hi again. 

  We have updates for this question from our team. Our team recommends you to use our PoN instead of yours. Or if you have ways to find out contaminated samples, we recommend checking your normals for tumor contamination and removing those samples from the PoN creation step. 

  Regards. 

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