SNP filtered out of results but not out of Manhattan plot

[joelle...@gmail.com]

I noticed some super significant SNP hits in my Manhattan plot that did not show up in the results tables. They were low MAF SNPs so were filtered out, but apparently they are not filtered out of the Manhattan plot. This might have been an intentional choice, I just thought to let you know in case you were not aware of this (or something else is wrong in my particular case, let me know if you want me to share the job ID). 

[Kyoko Watanabe]

Hi,

I am sorry for the slow response.

It could be filtered by MAF but SNPs that are not present in the selected reference panel also get filtered out, so it's most likely either of that.

In addition to that, FUMA also checked alleles and if the input alleles don't match with the reference panel, they are filtered out from the clumping.

Please let me know your job ID as well as your input for SNPs you are expecting in the results (so that I can check if the allele mismatch is the case here). 

Best,

Kyoko