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Somatic mutation not being called as somatic

rnaharrnahar SingaporeMember


I am using Mutect to call somatic variants in my sample from a known EGFR mutant patient. I find that the EGFR mutation is rejected by mutect. The extended output gave the reason being "alt_allele_in_normal". I see 5 reads out of total 153 reads in the normal supporting the variant allele (which could also be due to tumor contamination in the normal). I want this mutation to be called as somatic. What parameters do I change during the mutect run ? I have attached the extended output for you to have a look.
Also is there place where I can find all the options which can be used in mutect run and the default values. Further I would like to know the default values for read count, allele frequencies cut offs in mutect used for calling variants in tumor and normal. The help menu of mutect (with -h option) does not give these and also the --enable-extended-output option doesn't appear in the help menu (found it in one of the threads so could use it). Is there a location where there is better documentation of all the parameters of mutect ?


  • rnaharrnahar SingaporeMember

    Ok I was able to call it as somatic by giving different values to the following parameters --max_alt_alleles_in_normal_count 6 --max_alt_allele_in_normal_fraction 0.05 --max_alt_alleles_in_normal_qscore_sum 200
    However knowing the default values for all the muTect parameters would be quite helpful.

  • I agree with Rahul, that a listing of default parameters should be very informative to start understanding the output.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi folks,

    We are in the process of consolidating support for MuTect and GATK, and we plan to produce the same comprehensive tool documentation (with detailed lists of arguments and their default values) for MuTect as there is already for GATK (see here for examples). Hopefully that will help with this type of problem.

  • amitmamitm Manchester, UKMember

    hi Geraldine,
    Is the documentation for MuTect coming out soon? I am processing a lot of tumor normal pairs and to rerun them in future (when I get to know the tune-able parameters from the documentation) would be troublesome. A list of the parameters with their default values would be really useful, even without a detailed doc. like GATK.
    The java -jar help flag is not of much help.
    many thanks,

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @amitm,

    Working on it now -- hopefully we'll get something out within another week or two.

  • teamcoopteamcoop Ontario, CanadaMember

    I look forward greatly to the forthcoming documentation. For now, just a note that you can get a list of all available MuTect command line parameters by running java -jar mutect.jar -T MuTect --help.

    I believe that if you run MuTect without specifying anything beyond the required command line you can extract default parameter values from the VCF output, i.e. from the field labeled ##MuTect="...". If those are not the actual parameter values used by MuTect, then someone please correct me.

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