There is a tutorial regarding how to use SAIGE (https://documentation.dnanexus.com/science/scientific-guides/saige-gwas-walkthrough), but here it was not mentioned the GATE (https://github.com/weizhou0/GATE#uk-biobank-gwas-results)

Former User of DNAx Community_19
Is it possible to advise on how to use GATE through SAIGE on dnanexus?

Comments

3 comments

Date Votes
  • Comment author
    Rachael W The helpers that keep the community running smoothly. UKB Community team Data Analyst

    Hi Ra S,

     

    The Gate link says

     

    Currently, the only difference between this and the regular SAIGE job is that for step1, two additional arguments are used

    eventTimeCol = ??,

    eventTimeBinSize = 1

    and

    traitType = ?survival?

     

    Would you like to expound on the difference between SAIGE and GATE, and why a researcher should choose GATE rather than SAIGE.

    0
  • Comment author
    Former User of DNAx Community_19

    Thanks, GATE is an additional code which enables SAIGE to handle time to event data.

    0
  • Comment author
    Ondrej Klempir DNAnexus Team

    It looks like the github page https://github.com/weizhou0/GATE#uk-biobank-gwas-results is in progress, as the uk-biobank-gwas-results section is missing and it is not clickable. It might be worth to contact the author directly.

     

    I went ahead and check the currently open issues and I think it has been discussed here: https://github.com/weizhou0/GATE/issues/1

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