Clarity on Variant Callers being "optimized for UMI-containing data"
If not an error, choose a category for your question(REQUIRED):
b) What does (......) mean?
I was reading https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant, and I noticed this bullet under the Amplicons section (so perhaps this only applies to amplicon data):
HaplotypeCaller and Mutect2 are optimized to expect UMIs (Unique Molecular Identifiers). If your data does not have UMIs, then they will not play nice with the callers.
Since when have these Variant Callers been "optimized to expect UMIs"? I've never seen any mention of this anywhere else. Also, why will non-UMI-appended data not play nice with the callers?
-
Hi, please note that your question was posted while the GATK Team was Out of Office.
Please repost any outstanding GATK issues and we will get to them if possible. Our first priority is solving GATK issues and abnormal results, see our support policy for more details.
Please sign in to leave a comment.
1 comment