Reference genome build file

[rezarahman12]

Dear eMAGMA team,
I've found that the link provided to download the Genome1000 reference file is not working. Could you please share African ancestry genome 1000 reference file so that I can run eMAGMA?
I appreciate your time and help.

Kind regards
Reza
QBI, UQ

[eskederks]

Hi Reza,
This is Zac's response.
"The African sub-population reference data for 1000G can be downloaded from MAGMA website (https://cncr.nl/research/magma/) (under “reference data”). But I don’t think it’s a good idea to run eMAGMA on samples with non-European ancestry since the eQTL data was derived from GTEx European-only samples. We would need to create new ancestry-specific annotation files. This is a limitation of the method". We might look into this in the future to allow this method to be used for other ancestries.