BQSR: using COSMIC for knownSites?

Hi,

I am planning to run MuTect2 on some tumor sample pairs. Of course I will put all the bundle files as BQSR's knownSites, but I wonder if it is a good idea to also put the current COSMIC variations as knownSites as well? Since the samples are cancer cells/tissue, it may be a good idea to avoid known cancer-causing variations from being seen as sequencing errors, but then I also fear it would cause too much false positives...

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by Sheila

Issue Number
806
State
closed
Last Updated
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Closed By
chandrans

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