Variant Set Expansion - Divergence in LD proxy number between FUMA result table 'Ind Sig SNPs' and its exports 'snps.txt'

[frederic...@gmail.com]

Dear Kyoko,

first at all, also thanks a lot for your beautiful program! It makes GWAS Finemapping almost too easy.
And especially the visualization and customization is very good.

I use it at the moment at the beginning of my finemapping pipeline. And I may found a problem with the
export of the Variant Set Expansion. The number of LD proxy SNPs of each Ind. Sig SNPs differs
between the online fuma Result table 'Ind. Sig. SNPs' (Screenshot A) and the merging of the exports
 'snps.txt' and 'IndSigSNPs.txt' (Screenshot B, last column 'nSNPs_FUMA'). I double checked
the merging in R.

I tried it at two different loci. Job IDs 30996 & 31042. Can you please take a look.

Thank you very much in advance

Best,
Frederick

--------------------------------------------------------------------------------------------------------------------
Screenshot A: FUMA online result table 'Ind. Sign. SNPs.'



Screenshot B: Merging in R of 'snps.txt' and 'IndSigSNPs.txt'

[Kyoko Watanabe]

Hi Frederick,

Yes, you are right, some of them are miscounted somehow.

I have updated some scripts so now it should count correctly.

You actually need to use "ld.txt" to count the number of SNPs in LD with each Ind Sig SNPs since snps.txt file only contain Ind Sig SNPs with the highest r2.

If you wish to update results of job 30996 and 31042, I can do so from server side, so please let me know.

Best,

Kyoko