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how to modify "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval

I want to locally run the mutect2-normal-normal.wdl with mutect2-normal-normal.inputs.json offered by broad institute github. I already downloaded needed files and changed gs link to absolute file path. however, there is one file named "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval", I dont know how to modify it. Does someone know about it or have some reading material about it?

Best Answer


  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @Angry_Panda Can you elaborate on how you are trying to edit it or if you are receiving an error while trying to use the file?

  • Hi @SChaluvadi ,
    I edited mutect2-normal-normal.wdl file, import "/local path/mutect2.wdl" as m2, instead of mutect2_nio.wdl. (I tested mutect2.wdl locally, it worked). Then, I edited mutect2-normal-normal.inputs.json file. change file's google bucket link to file's local path. But, I dont know how to modify the content of this list: "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list".

    I tried to run workflow without giving a interval list, but it already ran 2 days, status: "[2019-08-05 10:23:51,75] [info] BackgroundConfigAsyncJobExecutionActor [21e422ddMutect2.M2:5:1]: Status change from WaitingForReturnCode to Done"

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    You can open the text file and make modifications to the intervals that you want to focus on. You should be able to use a text editor like Sublime or vim to open the file on your local machine and make modifications. If you are asking about content wise which intervals to leave in and take out, that would be based on what you are trying to achieve in your analysis - perhaps focusing on a chromosome?

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