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Mutect2 --artifact_detection_mode
blueskypy
Member ✭✭
hi,
could anyone share how Mutect2 identifies artifacts? I suppose those are from sequencing/mapping errors.
Thanks!
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Best Answer
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Geraldine_VdAuwera
Cambridge, MA admin
"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.
Answers
"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?
Issue · Github
by shlee
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.