UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS
When checking the UMI_METRICS output file from `UmiAwareMarkDuplicatesWithMateCigar`, I found that DUPLICATE_SETS_WITH_UMI > DUPLICATE_SETS_IGNORING_UMI.
What it means? I expected that when using UMIs, the number of real duplicates is lower, since it is able to distinguish between PCR duplicates and different molecules.
|DUPLICATE_SETS_IGNORING_UMI||Number of duplicate sets found before taking UMIs into account|
|DUPLICATE_SETS_WITH_UMI||Number of duplicate sets found after taking UMIs into account|
I found this explanation but I don't understand it completely.
Thank you for your post, Miguel Grau! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
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Thanks, Genevieve. Any update?
Besides the main question, when using UmiAwareMarkDuplicatesWithMateCigar, the pipeline is the same as usual? ie:
BAM -> UmiAwareMarkDuplicatesWithMateCigar -> BaseRecalibrator -> ApplyBQSR -> Mutect2 -> LearnReadOrientationModel/GetPileupSummaries/CalculateContamination/FilterMutectCalls.
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