MungeSumstats on GWAS data from non-Europeans

[MC4R]

Hi,

Thank you very much for this wonderful tool. Could MungeSumstats::format_sumstats be used on GWAS data from non-European populations? Thank you.

Cheers
Dev

[Al-Murphy]

Hey Dev,

Yes MSS should be able to handle non-European data without a problem. The reference datasets it uses could be the only place there could be an issue. These are:

• reference genomes GRCh37/GRCh38 for checks like is the NSP round on the reference genome (reference allele) and inferring the genome build
• dbSNP differing versions for checks like is the SNP present in dbSNP version of interest (based on RS ID/position & reference/alternative allele) and imputing any missing data for the SNP

Overall, this will not cause an issue as both the reference genome and the dbSNP databases account for non-European versions. If you want to be specially careful, just use the latest version of dbSNP we have v155 (it's the default) and read MSS's output messages to make sure a lot of SNPs aren't removed as they aren't found.

Thanks,
Alan.

[MC4R]

Thank you very much, Alan! Very helpful.

Cheers,
Dev

[Al-Murphy]

Great! Closing for now, if you have any specific issues please do ask in another issue.

Cheers,
Alan.