Somatic Mutation and PON creation

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avrajit

• July 15, 2021 05:01

To identify somatic mutation Mutect2  need 3 items

1. matched tumor-normal sample

2. a germline  variant of population data e.g. "somatic-hg38_small_exac_common_3.hg38.vcf"

3. And a Panel of Normal which I can make as per my choice.  My question is do I only include the Normal samples from tumor-normal cohort or I can also include some extra normal samples from some unrelated healthy individuals?  

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  Genevieve Brandt (she/her)

  • July 15, 2021 16:34

  Hi avrajit,

  I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic 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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  Pamela Bretscher

  • July 15, 2021 16:44

  Hi avrajit,

  As long as the normal samples are similar preparation and sequencing methods to the tumor samples, it is encouraged to include normal samples from healthy individuals as a larger panel of normals will generally improve the accuracy of variant calling. You can reference our documentation on creating a panel of normals here.

  Kind regards,

  Pamela

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  avrajit

  • July 16, 2021 04:06

  Hi Pamela,

  Thanks for your response. I also thought the same. Just looking for a confirmation. Thanks a lot.

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