error when there is NA for allele frequency

[jielab]

error when there is NA for allele frequency

[pjvandehaar]

Please send screenshot of error, file, and pheweb -v

…

On Sun, Oct 24, 2021 at 2:35 AM Jie Huang ***@***.***> wrote: Hi, there: I got a pheweb error when my GWAS's "af" column has NA values, sometimes all NA values. Is there a way to accommodate NA values for "af"? Thank you & best regards, Jie — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#182>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGSPCPQWPNQAZXHU5ABENTUIOZMDANCNFSM5GTEVZ7A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[jielab]

Dear Peter:

The error message is simply a short line of text. You will easily replicate this error, when your input GWAS has a column named "AF" with all NA values, and then your config.py file has 'AF': 'af'. Then Pheweb will complain that AF is not numerical.

The add_rsID function is really cool. Previously I commented that you guys could simply add a brief line to the end of your add_rsid.py script so that it does not force REF/ALT in your GWAS must be the same as that in the so-called reference genome. Most GWAS these days don't have REF/ALT, but only EA/NEA or A1/A2. It would be good that you guys could make add_rsid.py to accommodate this. Right now, most rsID are still missing even after add_rsid.

Finally, since pheweb could add_rsID, is it possible to add_Chr&POS if the input GWAS only has rsID?

Best regards,
Jie