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Oncotator output from 1.8 and 1.9

Haiying7Haiying7 Heidelberg, GermanyMember

Are the 2 versions giving same output?
The columns in the output files from the 2 versions are the same, right?

Best Answer

Answers

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @Haiying7,

    I've contacted our Oncotator expert about your question and I hope they will get back to you soon. If you have a choice, then the general recommendation is for you to use the latest version of a tool as it fixes bugs and typically has other improvements.

  • shleeshlee CambridgeMember, Broadie, Moderator

    @Haiying7, our developer says the following to your question.

    That really depends on the datasources used. I would recommend updating the data sources when migrating from Oncotator 1.8 to 1.9, so the columns would change.

  • Haiying7Haiying7 Heidelberg, GermanyMember

    But the data source did not change for more than one year. The one I downloaded last year:
    oncotator_v1_ds_Jan262015.tar.gz

    If this is not the newest version, could you please point out where I can download the newest version?

    Issue · Github
    by shlee

    Issue Number
    1575
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    sooheelee
  • Hi @shlee,
    I've downloaded oncotator_v1_ds_April052016.tar.gz, but I've some problems with the extraction of the files. In details, I am able to extract (using the following command: $ tar zxvf oncotator_v1_ds_Jan262015.tar.gz) only the following folders: 1000genome_db, achilles, cancer_gene_census, ccle_by_gene, ccle_by_gp, clinvar cosmic, cosmic_fusion, cosmic_tissue, dbNSFP_ds. After that, I have several errors as shown in the screenshot in attachment.
    Could you kindly help me?

    Thanks in advance

  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @ornella,

    From where are you downloading oncotator_v1_ds_Jan262015.tar.gz? Can you try the oncotator_v1_ds_April052016.tar.gz version from the GATK bundle?

    Fyi, we are working on an updated version of Oncotator, called Functotator. Funcotator is in beta release currently but we'd love for folks to try it out and give us any feedback they have.

  • Hi @shlee,
    sorry, I misspelled. I've downloaded from the GATK bundle oncotator_v1_ds_April052016.tar.gz and I have the errors above when I extract it both using the command $ tar zxvf oncotator_v1_ds_April052016.tar.gz and a decompression tool. Can you help me to understand the problem?

  • shleeshlee CambridgeMember, Broadie, Moderator
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