How can I use 1000G LD reference to perform MTAG based on GWAS from non-EUR population

[jianvhuang]

Hi, I wonder if MTAG use the LD reference file in ld_ref_panel folder, even if I do not specify the --w-ld-chr command. I would like to apply MTAG to GWAS from non-EUR population, how can I prepare the non-EUR 1000G LD reference for my analysis, e.g. EAS, SAS?

Thank you.

[JonJala]

Yes, if the panel is not specified, it uses the eur_w_ld_chr included in MTAG by default. You should be able to generate an LD score panel using the ldsc_mod code included with MTAG if you want to make your own.

On Wed, Jun 8, 2022 at 9:21 PM jianhuang @.***> wrote:

Hi, I wonder if MTAG use the LD reference file in ld_ref_panel folder, even if I do not specify the --w-ld-chr command. I would like to apply MTAG to GWAS from non-EUR population, how can I prepare the non-EUR 1000G LD reference for my analysis, e.g. EAS, SAS?

Thank you.

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