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jianyangqt / gcta

GCTA software
GNU General Public License v3.0
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Input multiple .sample files #68

Closed chenpunk closed 6 months ago

chenpunk commented 6 months ago

Hello, I'm a novice at GWAS and now I'm trying to perform a mlm association test using UKB imputed data with your tools. However, I have met some problems when generating a GRM:

Options:

--mbgen chr.list --make-grm --out OUTPUT

Note: GRM is computed using the SNPs on the autosome. Error: no phenotype file presents An error occurs, please check the options or data

It seems that I need a .sample file when inputing bgen files. But there are 22 .sample files corresponding to each autosomes and the command '--sample' is not able to handle all of them. So is it possible input multiple .sample files? Or, should I generate GRM chromosome by chromosome and use command '--mgrm' to merge them all together? I hope you can give us some advice.

chenpunk commented 6 months ago

It strikes to me that .sample file contains information of all individual so that all .sample files should be same. Sorry for my silly question. I will close the issue