Sensitivity analysis for GATK CNV PoN

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Kimal Rajapakshe

• March 29, 2021 21:51

Hi,

I'm generating a CNV panel of normals following the directions in "(How to part I) Sensitively detect copy ratio alterations and allelic segments". 

In step 2, the tutorial mention Ideally, researchers should perform a sensitivity analysis to choose an appropriate value for this parameter. See this related discussion.

Anyhow, above link is not working for me. Can you please help me to access above link?

Best,

Kimal.

 

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• Official comment

  

  Genevieve Brandt (she/her)

  • April 02, 2021 19:36

  Hi Kimal Rajapakshe,

  The discussion was at our old forum site, which has been deactivated. The information has been preserved in this legacy site, that you can use when you are looking for information about older GATK versions that we no longer support: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/

  Here is the link to that discussion: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2018-04-11-2017-12-02/11461-GATK-4012-No-nonzero-singular-values-were-found-in-creating-a-panel-of-normals-for-somatic-CNV

  Best,

  Genevieve

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