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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 can the difference between Mutect2 FORMAT fields FAD, F1R2, F2R2, SB and AD be explained?



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    Genevieve Brandt (she/her)

    Hi Eva König,

    Thank you for your question!

    AD and SB are a read based annotations while FAD, F1R2, and F1R2 are fragment based annotations. Fragment counting does not double count paired reads that overlap. So if your paired reads never overlap, the numbers will be equal and if your paired reads always overlap, the fragment counts will be half the read counts. In most situations, some reads overlap but not all.

    Let me know if you have any further questions.



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    Eva König

    Thank you Genevieve-Brandt-she-her your answer was very helpful.

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    Vincent Appiah


    In my info fields I have F1R2 and F2R1.  

    Is this expected or only one of them is supposed to be there.?



    The samples were sequenced in two lanes. So I merged them before running mutect2

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