effect allele when creating your own instance of PheWeb

[Jennifer Huffman]

Hi!

  In the github documentation for prepping your own association results for use in PheWeb, I can't find anywhere where it defines if the allele frequency, beta, and odds ratio is referring to the reference or alternate allele. Since this is something that varies across software I wanted to reach out. Is that something that matters for the code, or something that we should just decide for ourselves and make clear in the documentation to our users?

Thanks,

Jenny

[pjvandehaar]

Hi Jenny,

PheWeb assumes that all of those are for the alternate allele.  Thanks, I just updated the README at https://github.com/statgen/pheweb/blob/master/README.md#3-prepare-your-association-files .  Let me know if you have other questions.