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We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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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!
Tagged:
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.