plink1.9 for meta-analysis

[Wenyu Song]

Hello, 

I have been using PLINK1.9 for GWAS on three different cohort (different micro-array chips and different population). I want to measure the association between SNPs and type2 diabetes (binary outcomes). I used --logistic option and control for PC1 and PC2. The QQ plot from each population looks good. Now I want to combine the .logistic files from three different population. I found some usage information of --meta-analysis on PLINK web and below is my code:

plink --meta-analysis  4784_T2DM_CUR.assoc.logistic 4927_T2DM_CUR.assoc.logistic 5352_T2DM_cur.assoc.logistic

According with the Hint on the web, I have added SE column in the .logistic file by specified --ci 0.95

But I kept getting the error like this:

Error: This flag's implementation is unfinished or unstable.  If you wish to test it, use the latest development build

I do not know if it is because of version issue or my format is still wrong 

Any help is appreciated!

Thank you 

Wenyu

[Christopher Chang]

What do you get when you type "plink --version"?  I'm guessing it's from 2014-15, and the error message will go away if you update to the latest stable build.

[Wenyu Song]

it is "PLINK v1.90b2q 64-bit (7 Dec 2014)"

I am using the cluster to do the analysis and they only have this version. For the latest build, is the link below the right version I can download? I am using MAC 

https://www.cog-genomics.org/plink/2.0/

Thank you very much!

[Christopher Chang]

For --meta-analysis, you'll want 1.9/ instead of 2.0/ .

[Wenyu Song]

I updated to PLINK V1.90b4.4 64-bit (21 May 2017) and it works now 

thanks a lot!

Wenyu