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?
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