about mutect2 alt_allele_in_normal

Hi, I ran mutect2 with the default setting. And I got all of the mutations marked "alt_allele_in_normal". I just want to know if this is OK? Should it be some of the mutations marked alt_allele_in_tumor?


  • EADGEADG KielMember ✭✭✭

    Hi @twotwo,

    this means that all variants which are found in your tumor sample are found in your matched normal too. Tumor specific/eclusive variants would have a "Pass" in the filter field if they dont get hit by some of the other filters of mutect2.

    Greetings EADG

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