Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

UmiAwareMarkDuplicatesWithMateCigar - UMI_METRICS



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    Genevieve Brandt (she/her)

    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. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Miguel Grau

    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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