Tumor in Normal contamination

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Ibel Carri

• April 05, 2022 16:16

I have some normal samples that I know are contaminated with tumor tissue and I would like to know the fraction of contamination.

Could it be possible to use the pipeline of CalculateContamination but instead of using a reference vcf of common polimorphisms, using a vcf of reported mutations in cancer?

Thanks!

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  Genevieve Brandt (she/her)

  • April 06, 2022 01:33

  Hi Ibel Carri,

  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,

  Genevieve

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  Genevieve Brandt (she/her)

  • April 13, 2022 02:15
  • Edited

  Hi Ibel Carri,

  Take a look at this Mutect2 whitepaper, it details the CalculateContamination tool in section III B. I think you will need to keep the resource as common polymorphisms because it is one of the key assumptions of the tool.

  I recently gave a detailed description of the tool in another forum thread: https://gatk.broadinstitute.org/hc/en-us/community/posts/4415927220635-CalculateContamination-differs-much-in-single-and-paired-mode

  Let me know if you have any other questions.

  Best,

  Genevieve

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