Hello, I recently saw this post: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant
- 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.
And I am wondering if someone can explain how mutect2 and haplotypecaller uses UMI information, and what do we need to do if we don't have UMI-duplexed sequence data?
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