What's the minimal number of normal samples required to generate the SomaticPanelOfNormals?
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This question was asked during the webinar on Nov 17, 2020. It is reposted here for posterity.
Q: What's the minimal number of normal samples required to generate the SomaticPanelOfNormals?
If I only have 19 samples will it be recommened to fuse my pon with the public GATK panels of normals 1000g_pon.hg38.vcf.gz?
A: You should typically see a lot of improvements in your calls with only 10 samples, but this is typically not enough. I recommend 40-100 samples. The more the better, but of course costs are always a concern, so it isn’t always possible to sequence that many samples.
- Mark Fleharty
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sorry, I accidentally delete my post.
The question was about how many samples where used for the 1000g_pon.hg38.vcf file creation.
Many thanks
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manolis here are some forum posts covering that file:
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