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Method: broadgdac/mutation_signature_analyzer

Hi! I'd like to try this method (https://portal.firecloud.org/#methods/broadgdac/mutation_signature_analyzer/19) on some of my samples that I analyzed using the best practices Mutect2 workflow. I have some mafs from that that I want to analyze for mutational signatures, and I have just a couple questions about the method configuration. Below I provided the default configuration.

1) What is the "tumor_type" variable referring to? I just want to know what file in my workspace or bucket to specify.
2) I assume "maffile" is my maf that I want to be analyzed - do I specify the maf file by providing a "gs://" etc link to the bucket, or can I specify the maf by specifying the attribute as like "this.oncotated_m2_maf"




  • ChipChip 415M 4053Member, Broadie

    tumor_type is jus the name of the sample_set (or pair_set if you specify pair_set in the "Root Entity Type" in the configuration) that you are processing with mutation_signature_analyzer. "maffile" is the maf file that you want to process for that sample_set (...or pair_set).

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @aboynton Additionally, the "this." notation tells FireCloud to look at your data model in the table you set as your root entity. If you set your root entity as "sample", the "this." will look at the sample data model. Since your maffile is not part of the data model, I would suggest using the direct path or you can set it as a "workspace." so that you can access it in any method that you may use in that entire workspace.

  • aboyntonaboynton Member

    Thanks for the help!! I've specified my root entity as pair and given the attributes for tumor_type and the maffile their corresponding designations in my method config:

    However, I get an error message after launching the analysis about the workspace package:

    Any idea what's causing this/what I need to do? Thanks!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hey @aboynton Can you check that the this.pkg__Mutation_Signature_Analyzer is the same exact label that is in your data model? I believe that method config inputs are case sensitive so the "pkg__Mutation_Signature_Analyzer" should be exactly the same as in your data model.

  • aboyntonaboynton Member

    Thanks! So looking into that now, it doesn't seem like I actually have these signature packages in my workspace. Basically, I originally exported the "broadgdac/mutation_signature_analyzer" method (https://portal.firecloud.org/#methods/broadgdac/mutation_signature_analyzer/19) to my workspace, and from there I've been specifying my pair data in the method config (as I took a screen shot of in my last post). But now I'm wondering if it's not working because I don't actually have these package files in my workspace or bucket. How do I get these packages into my workspace/data model? I don't see any "gs://" file link to the packages that I could like upload into my own workspace bucket to then specify as an attribute. Thanks!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @aboynton Since the method was most likely part of a workspace previous to being added to the method repository, it would be best to contact the author of the Method to get details on what the packages are and where to get them. If you notice, some of the attributes are "workspace." which means they were listed in their workspace attributes that we can't see. Let me know if we can help direct you further on this issue.

  • aboyntonaboynton Member

    Thanks I'll email them and see what they say!

  • aboyntonaboynton Member

    Hi! So, I've emailed the method owners and also GDAC but haven't heard back from anyone about this. Do you know of anyone else that might have some insight as to how to track down these method package files?

    Alternatively, is there some other more updated method or workspace for mutation signature analysis on Firecloud I'm missing? Thanks!!

  • birgerbirger Member, Broadie, CGA-mod ✭✭✭

    @dheiman should be able to provide assistance.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    Hello @aboynton - Unfortunately, we do not have much information about methods that our own team hasn't uploaded to the repository. You can try to send a follow up email to the authors of the method. We also don't have any additional information other than what you can search in the method repository so other than searching, we wouldn't be able to tell you if there are other methods for mutation signature analyses. If you would like, you can peruse through our Featured Workspaces to see if any of them can be used for your use case!

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