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

How do I add allele depth to Mutect2 output?



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    Genevieve Brandt (she/her)

    Hi Ashi,

    Thank you for your question! This question falls outside of the scope of GATK Support. (See our support policy for more details). However, we encourage you to keep posting questions because they help us improve our documentation and build resources. In addition, if you know the answer to other questions outside of our GATK support team scope, please help out other users! And other users feel free to chime and discuss here.

    Mutect2 is a popular topic on the forum so we wrote an FAQ article answering many of the questions posted in the last year. Please see that article, as well as our other comprehensive documentation, in case your answer is there.

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    David Benjamin

    Ashi Mutect2 emits the AD genotype field for each sample.  Is that what you want?

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