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cfDNA analysis using GATK

Dear experts,

May I consult with you that if GATK pipeline can be used to call mutations for the cell-free circulating DNA sequencing data? If so, is there any difference or any points to pay attention to?

Thank you very much in advance!


Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    edited November 2015

    Hi there,

    This is not something we have tried ourselves so we can't give you any canned advice. I would expect you'd have to deal with a number of complications (related to coverage, purity etc) depending on what you are trying to learn from the cfDNA data. Can you give us a bit more context on your use case / experimental design?

  • rxy712rxy712 Member

    Thank you for your response! I got a data set, including 30 patients with plasma cell free DNA and matched PBMC DNA as an internal control that reflects the genomic DNA from the patient. I need to call somatic mutations for these patients. I guess I can use bwa-picard-GATK realignment and recalibration pipeline and switch to MUTECT or other tools for variant calling. Am I right? Any input is very appreciated!

    Issue · Github
    by Sheila

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  • rxy712rxy712 Member

    Yes, I did what you said. Thank you! It is good to know that MuTect2 can do both SNV and indel now.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    FYI mutect2 is now available in the newly released version 3.5

  • namratapatelnamratapatel AnandMember

    I have cfDNA samples of 4 patients and we have taken two normal samples, now how can i call variants using Mutect2 if i dont have matching normal and patient pairs?

    Thank You

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @namratapatel

    Please follow this doc for info on variant calling with mutect2 without matching normal and patient pairs.


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