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Gero Doose

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Latest activity by Gero Doose
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    Gero Doose commented,

    1. Community
    2. Somatic
    3. Mutect2 - sum of FAD greater than sum of AD

    Hi David Benjamin, Thank you for providing such a thorough explanation! Your response has significantly clarified my understanding of how even non-overlapping read pairs can impact somatic genotypi...

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    Gero Doose commented,

    1. Community
    2. Somatic
    3. Mutect2 - sum of FAD greater than sum of AD

    Hi David Benjamin, Thank you very much for providing a possible explanation! If I understand correctly, this occurs when overlapping read pairs are merged into one more informative long read (repr...

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    Gero Doose commented,

    1. Community
    2. Somatic
    3. Mutect2 - sum of FAD greater than sum of AD

    Hi SkyWarrior, Thank you for your explanation. Indeed, FAD refers to the fragment counts while AD refers to read counts. The case where I would expect those values to be different is on overlapping...

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    Gero Doose created a post,

    Mutect2 - sum of FAD greater than sum of AD

    1. Community
    2. Somatic

    Dear community, In a VCF file generated by the GATK Best Practices MuTect2 pipeline, I've observed 681 out of 27084 lines where the sum of the Filtered Allelic Depths (FAD) is greater than the sum ...

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