loss of original variant identifiers in FUMA v1.6.0

Skip to first unread message

Lam-Ha Dang

Sep 8, 2023, 1:30:53 PMSep 8
to FUMA GWAS users
Just a comment for consideration:

My data is in Hg38 and used FUMA's new feature of mapping in Hg38 coordinates. I've supplied a column in the rsID parameter to keep track of the variant identifiers (not in rs# format) in my original data (Hg38) to merge with my other result files in Hg38. 

This new version of FUMA replaces my original identifiers with dbSNP "rs" identifiers and positions in the output are in Hg19, thus I've lost all mapping to my original data. In the past, FUMA kept the original identifiers if a column was supplied to the rsID parameter. It would be useful to have the ability to keep the original identifiers.

Thank you,


Sep 11, 2023, 5:04:14 AMSep 11
to FUMA GWAS users

Thanks for your comment, that is a good point. I chose to code the new feature to remove the column that users designated as the rsID column to avoid FUMA using this column to overlap variants with the reference panel. Allowing user designated ID columns for output is a good idea but would require an extensive change to FUMA.

I can make the GRCh38 unique ID (chr:pos:a1:a2) to rsID file that the new update uses downloadable. Then you will be able to see which of your variants were being mapped to rsIDs. 

I will make a note of your comment and think about the best long term solution to this issue. 


Lam-Ha Dang

Sep 14, 2023, 11:41:54 AMSep 14
to FUMA GWAS users
Hi Doug, 

Thank you for getting back to me. That 'short-term' solution sounds perfect. I'm glad that the implementation was doable on your end.


Reply all
Reply to author
0 new messages