pan-metastasis's Issues
Cutoff threshold for FFPE samples
Dear authors,
Thank you for your fabulous work and for sharing your relevant code. I successfully applied the FFPE_artifact_01.R script to our FFPE samples and obtained FoxoG values for all the SNVs. I have the following questions:
- What is the threshold cut-off you considered to call an sSNV an artifact?
- In the FFPE_artifact_02.R script, I noticed that the filtering was based on the OxoGCut annotation. Could you direct me to the annotation resource or approach to obtain these values for my data?
Thank you very much for your help!
Best,
Prashanthi D, PhD
Postdoctoral researcher at UCLA
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