panel of normals for mutect2
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29 days ago
lait ▴ 160

Hi,

We run several WES projects on human samples.one of the projects is a trio project, where we sequence a mother, a father and a child with cancer (we sequence tumtor and normal samples for the children).in a second project we sequence only children (without parents) who have specific types of cancer and get specific types of treatments. So each project tries to investigate a different research subject.

I have two questions in this regard:

  1. to construct a PoN for project 1, I need to use the normal samples of the children. Can I also include the samples from the parents too ?
  2.  can I use a unified PoN for both projects ? or should each project has its own PoNs? in other words, what criteria should I look for, regarding which samples to include in the same PoN, other than that the samples should be sequenced using the same sequencer, and the same capture kit should be used?

thanks !

mutect2 gatk NGS PoN somatic • 104 views
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