germline vs somatic CNV GATK calling
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20 months ago
cocchi.e89 ▴ 230

I was wondering about the theoretical differences and use-case applications for the 2 different GATK CNV calling pipelines: germline and somatic

I know that the somatic should be more sensitive than the germline but let's consider 2 real use-case scenario:

  1. potentially pathogenic CNV discover in a particular disease (let's say a rare disease): would it be better to first generate a PoN and then call cases against it with the somatic pipeline? Or generate a cohort and use case-mode against it with the germline one?
  2. analysis of all ploidy changes and CNV in an immortalized cell-line (so theoretically a lot): somatic or germline?

Also the somatic one produces very great plots that the germline does not. Why is that?

Thank you so much in advance for any help!

CNV germline somatic GATK WGS • 803 views

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