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Mutect2 --mitochondria-mode .args file?

ajwilsajwils Baltimore, MD -- JH GenomicsMember
Relatively new to GATK and I'm looking to follow your double alignment strategy for the mutect 2 mitochondrial variant calling. I'm mainly working at the linux command line. Is there a usage example on how to setup the -I .args input file referenced in the GATK readme? Would it basically just be identical to the example input json file in the mito pipeline workflow?

Answers

  • ajwilsajwils Baltimore, MD -- JH GenomicsMember
    Or perhaps I'm misunderstanding the inputs. Does this need a .args file?

    Is there a command line usage example that would replicate the full wdl pipeline?
  • florian_huberflorian_huber SwitzerlandMember
    Hi @ajwils ,

    I hope hat you found out how to run Mutect2 by the time.

    Here is a basic example on how to run Mutect2 once you have installed GATK. Please note that the following command line refers to GATK4.1.3.0 (Mutect2 arguments might vary depending on the version of GATK that you're using, you have to look at the tool page)


    gatk Mutect2 \
    -R reference.fasta \
    -I germline.recalibrated.bam -I tumor.recalibrated.bam \
    -normal germline_name \
    --germline-resource gnomad_file \
    --f1r2-tar-gz tumor.f1r2.tar.gz \
    -O tumor.mutect2.unfiltered.vcf

    I hope this helps

    Regards,

    Florian
  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited October 2019

    @florian_huber Thank you so much for your input! I hope you continue to support the GATK community. GATK team is grateful for your time and support.

    @ajwils as Florian mentioned above, take a look at the tool documentation here: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php

  • ajwilsajwils Baltimore, MD -- JH GenomicsMember
    edited October 2019

    @florian_huber said:
    Hi @ajwils ,

    I hope hat you found out how to run Mutect2 by the time.

    Here is a basic example on how to run Mutect2 once you have installed GATK. Please note that the following command line refers to GATK4.1.3.0 (Mutect2 arguments might vary depending on the version of GATK that you're using, you have to look at the tool page)

    gatk Mutect2 \
    -R reference.fasta \
    -I germline.recalibrated.bam -I tumor.recalibrated.bam \
    -normal germline_name \
    --germline-resource gnomad_file \
    --f1r2-tar-gz tumor.f1r2.tar.gz \
    -O tumor.mutect2.unfiltered.vcf

    I hope this helps

    Regards,

    Florian

    It took me a few weeks of research but I actually answered my own question. While I already understood how to run Mutect2 at the command line (and thank you for the attempt to help), the real issue was 'how do I run the mito variant calling wdl pipeline at the command line'? I was assuming that --mitochondria-mode implemented the wdl pipeline and performs the double alignment. It does not. All it does is set some settings like tumor-lod.

    In short, you can't easily run the wdl pipeline in a compact bit of code just via the GATK command line. The wdl pipeline scripts are calling dozens of different gatk operations, with several file intermediates, and all the alignment and quality control steps are handled internally. While you can certainly take the terra wdl pipeline output vcfs, copy paste the generated command line input, and attempt to reverse-engineer everything the scripts are doing locally, it is just not worth the hassle.

    The easier solution to run the pipeline is to either run on Terra, or run locally with Docker/Git/and Cromwell (which is what I'll probably ultimately do).

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