allele

[ooozcl]

Hi paturley, There is no freq column in my summary data. I see that in other posts, you mentioned using the reference population to calculate MAF. I used 1000G data to limit SNP to SNP in summary, and calculated the MAF value, but I found that some SNP alleles in 1000G are opposite to those in summary. Which one should prevail? can you give me some suggestions? thank you.

[paturley]

You should make sure that the allele frequency that you merge into your GWAS data corresponds to the effect allele in the GWAS. So you should use 1-MAF from the 1kG data for discordant SNPs. You could also switch the reference allele in you GWAS data, but you'd also need to switch the sign of the beta. Feels a bit more error-prone to me.

On Tue, Dec 7, 2021 at 8:01 AM ooozcl @.***> wrote:

Hi paturley, There is no freq column in my summary data. I see that in other posts, you mentioned using the reference population to calculate MAF. I used 1000G data to limit SNP to SNP in summary, and calculated the MAF value, but I found that some SNP alleles in 1000G are opposite to those in summary. Which one should prevail? can you give me some suggestions? thank you.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/150, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5KSRE55SKER3OPZHUDUPYATFANCNFSM5JRGGIRQ . 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.

[ooozcl]

Thank you for your advice！

[ooozcl]

Hi paturley, I have another question. I see a literature that calculates the genetic correlation of diseases and traits associated with AD. Only family history has a high correlation. Is it appropriate to use MTAG analysis in this case?