ERROR:005

Anastasia G

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Aug 31, 2021, 11:34:35 AM8/31/21

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Hello,

Similarly to other users, I have a recurring ERROR:005 message stating that "No significant SNPs were identified". I have tried all the suggested changes (using the least stringent p-value threshold, unchecking the MAGMA analysis, decreasing MAF threshold) but nothing seems to be working. I have checked the top 10 SNPs in each input file and it seems that there are indeed some significant SNPs (e-12, e-13, e-16).

Here are the jobIDs of the original jobs, using the default parameters:

143054

143058

143059

Any advice would be really useful. Thank you for your time.

Best,

Anastasia

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

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Sep 6, 2021, 10:33:18 AM9/6/21

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Hi Anastasia,

I looked at job 143054 and the variant on chr 4 pos 83668997 should have been included. It exists in the reference and is below your threshold. Can you share with me the line of your input file for this variant?

It is possible that your SNPID column might be causing an issue but I do not have access to the original input file to check.

Cheers,

Doug

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

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Sep 8, 2021, 4:25:40 PM9/8/21

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Hi all,

The issue was discussed by email. The problem stemmed from the input file having a different position for the same variant (based on rsID) than FUMA. The rsID was checked in dbSNP and the position of the input file was different to the GRCh37 position in dbSNP. dbSNP and FUMA shared the same GRCh37 position for that variant.

Cheers,

Doug

Anastasia G

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Sep 15, 2021, 4:35:07 AM9/15/21

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Hello Doug,

Sorry for the late reply. By changing the SNP positions the problem was fixed indeed. Thank you very much for your help.

Cheers,

Anastasia

Junhao Wen

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Jan 28, 2022, 12:35:48 PM1/28/22

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I had the same problem. How did you correct the SNP positions caused by different versions of GRCh37 and 38? Liftover? Can this work directly with the GWAS summary statistics files?

THANKS

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

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Jan 31, 2022, 7:05:52 AM1/31/22

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Hi

You can get the liftOver executable (https://genome-store.ucsc.edu/) and the chain files (http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads) from UCSC. There is also a wiki which might be able to help you with the syntax (https://genome.sph.umich.edu/wiki/LiftOver#Lift_genome_positions).