could anyone share how Mutect2 identifies artifacts? I suppose those are from sequencing/mapping errors.
"artifact_detection_mode" really just means "call everything that moves" -- it's used to generate the PON from normal samples. If several normals in a PON share the same low-frequency calls, they're probably artifacts. So if you provide that PON to M2 when it's doing the calling on the T-N pair of interest, calls that are represented in the PON will be filtered.
This mode can also be applied to tumor samples as a primitive tumor-only calling method but the output is loaded with false positives and must be filtered stringently.
Thanks! Here is the line > "If several normals in a PON share the same low-frequency calls, they're probably artifacts."
How come I don't see the "select as answer" option?
Seems the Vanilla site is experiencing a number of oddities. Thanks for letting us know.
For some reason (probable oversight on my part) the category settings allowed you to post this as a "Discussion" instead of as a "Question". Only the latter type gets the "select as answer" option. Switched the type and fixed the setting so this should be all good now. Thanks for the report.