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

The missing value in Mutect2 vcf

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    Genevieve Brandt (she/her)

    Hi Hsu Pei-Chun, were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.

    If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.

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    David Benjamin

    Hsu Pei-Chun This is the correct behavior.  Mutect2 does not emit a QUAL or ID.  You need to run FilterMutectCalls to get the FILTER field.

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