I am looking at the challenge 1 training data for the MuTect2 variant calls, and was wondering if there was a difference in protocols between patients. Based purely on the line count of each of the files in the training set, there seems to be 2 distinct groups. Is there any experimental or processing differences between patients in that folder? Ex. MMRF_1634 and MMRF_1646 have 3,754 and 18,887 variants respectively.
Created by Nicholas Smith smithnickh Hi Nicholas - apologies for the delay. If you are using the `WES_mutationFileMutect` field, all samples were processed with the same pipeline for consistency. That said, not all samples have same quality, tumor purity and coverage. Due to such differences between samples you may end up seeing more variants in one samples (e.g., has better coverage across most regions) compared to others. I hope this addresses your question, let me know if you need me to elaborate further.
Best,
Fadi Hi Nicholas,
A collaborator should be answering this shortly.