Not recognised SNPs

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Serafi Cambray

Jul 20, 2023, 5:18:07 AMJul 20
to FUMA GWAS users

I realised that some SNPs are not considered for analysis, for example rs34366210 or rs2291739. 

I don't know if it is common or just few SNPs are not recognised. 

Do you know wichis the aprox. % of missing SNPs and why are they not considered? 



Jul 20, 2023, 5:59:56 AMJul 20
to FUMA GWAS users

One of the main reasons that variants are dropped is that they are not present in the reference panel. The variants need to be in the reference panel so LD information can be used to define genomic risk loci. You can download the list of variants included in the reference panel here

There are some other reasons why variants are dropped:
  • They have a MAF lower than the threshold chosen in the submission page
  • They have duplicate IDs
  • The information in the row for that variant could not be parsed (strange formatting)
  • The information in that row for that SNP does not match the reference panel (conflicting rsIDs).
How frequently variants in your data are not included in FUMA depends on your data. In the future, we are hoping to add output of which variants were not included in the analysis to improve clarity around this. 


Serafi Cambray

Jul 24, 2023, 7:21:50 AMJul 24
to FUMA GWAS users

El dia dijous, 20 de juliol de 2023 a les 11:59:56 UTC+2, va escriure:
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