Not recognised SNPs

Serafi Cambray

unread,

Jul 20, 2023, 5:18:07 AMJul 20

to FUMA GWAS users

Hi,

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?

Regards,

Serafí

d.p.wi...@vu.nl

unread,

Jul 20, 2023, 5:59:56 AMJul 20

to FUMA GWAS users

Hi

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 https://fuma.ctglab.nl/tutorial#refpanel.

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.

Cheers,

Doug

Serafi Cambray

unread,

Jul 24, 2023, 7:21:50 AMJul 24

to FUMA GWAS users

Txs!!!

El dia dijous, 20 de juliol de 2023 a les 11:59:56 UTC+2, d.p.wi...@vu.nl va escriure:

Reply all

Reply to author

Forward