Inquiry Regarding Mutsig2CV Results with Large MAF File

[ShinXeno]

Hi,
I am writing to seek clarification regarding the results I obtained while using the Mutsig2CV software with a MAF file containing 220,000 mutations and 1,900 tumor samples from WES data. By using the default parameters, I observed a huge number of significant genes (12,784 out of 18,862, q value<0.1).

I am wondering if this outcome could potentially be attributed to the software itself, or if there might be some factors I should consider to improve the accuracy of the results. Your expertise and insights would be greatly appreciated in this matter.

Thank you for your time and assistance. I look forward to hearing from you and receiving guidance on this issue.

[julianhess]

A few things to consider:

• Is the MAF completely clean of artifacts?
  • Are the samples fresh frozen? FFPE?
  • Is there potential germline contamination in the MAF?
• Are there multiple tumor samples from the same patient in the MAF?