More ancestries as download option?

[swvanderlaan]

Is it possible to also add the other ancestral groups to the download?

• SAS
• AFR
• AMR
• ALL or PAN for all the populations (handy for multi-ancestral populations GWAS) and/or a function that would enable to combine a given set of downloaded references (e.g. EUR and EAS) into one reference for GWAS with a specific number of ancestral groups

[swvanderlaan]

Happy to help create the datasets if you tell me how to exactly do this?

[Cloufield]

Hi, Thanks for the suggestion! Actually the raw 1KG dataset was processed using the code as described in https://cloufield.github.io/gwaslab/Reference/#1000-genome-projecthg19. You can easily prepare the dataset for your purpose. I will update the datasets for the population you mentiened soon (previous the datasets were hosted on Dropbox with limited storage and recently we upgraded the storage).

[swvanderlaan]

Thanks. I am making those files now, as per instruction. Does take a while... :-)

[swvanderlaan]

Ok. I got them all, except for the PAN/ALL dataset, i.e. the one including all 1000G variants to use as a reference when doing a trans-ancestry analysis. It takes up a lot of intermediate/temporary space for the last step (merging) which I don't have at the moment. Did you happen to upload that one, by any chance?

[Cloufield]

Hi, Sorry for the late reply. I have updated the reference datasets including all populations and PAN datasets. (Indeed it took very long and a lot of space to merge the datasets...) Since the links for Dropbox have changed, I have also updated the parsing. To download the new datasets, please update to v3.4.24.

Please note that the PAN datasets are large (>10GB)

[swvanderlaan]

Oh wow! Thanks a lot!