I want to ask several question about this tool.

q1: Mutect triages sites based on their pileup at a single base locus; here you mean look each base step by step. but what is the standard of triage, and the pileup refer to what accumulates.

q2: pairHMM used in germline haplottypecaller, but in somatic just simply focus on base quality, is it good enough?

q3: we can now estimate the likelihoods of no variation and of a true alt allele with allele fraction f.

is allele fraction f refer to AF or POP_AF in vcf file ? or neither?

q4: The likelihood of no variation is the likelihood that every alt read was in error. in error means the likehood value is not big enough?

q5: where we again assign infinite base quality to ref reads, but you have said that "you use base quality instead of pairHMM", if is infinite, is it fair to ref base?


  • picard_gatk_mjpicard_gatk_mj Member
    edited December 2018

    here said mutect2 use pairHMM, is this contradictory? red circle label in the bottom left
    thanks a lot

  • manbamanba Member ✭✭
    1. Identify ActiveRegions
      The program determines which regions of the genome it needs to operate on, based on the
      presence of significant evidence for variation in the tumor sample versus the normal sample.

    “based on the presence of significant evidence ” means more reads different fro ref, how is the significant defined? is there a p value, just like 0.05 in statistics frequency?

    thanks a lot

  • manbamanba Member ✭✭

    and I think gatk4 supply tumor-only mode, how it will do the step need normal of th four steps?
    thanks a lot.

  • manbamanba Member ✭✭

    anyone helps, thanks a lot

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @manba

    All these topics are well explained in the documents are you referencing from. These documents are written by subject matter experts. We try and help users with usability issues with gatk tools. For example, errors or bugs users face while using gatk tools. So if you have any questions regarding that then please reach out to us, but only after you have read all the tool documents well.

    We have been receiving a large volume of questions from you. Please try and ask fewer and more relevant questions. When posting questions by following the guidelines outlined in We ask this because we have multiple users to cater to and we do no want to spend so much time on one user that the other users feel neglected.

    Given your many questions, I think you may benefit from attending a GATK bootcamp. Our bootcamp/workshop schedule is at You can also ask your institute to schedule a GATK workshop or try to attend a GATK event at an ASHG or AGBT conference. In leiu of attending a workshop, I'd like to point you to GATK workshop materials under the Slides and workshop tutorial bundles section on the Presentations page. On this page you will also find links to YouTube videos that explain GATK tools and background context, including the entirety of workshop presentations. I think you will find these helpful.

    Also please refrain from using multiple accounts for a single user, i.e. @manba, @mesi and @picard_gatk_mj


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