ERROR:006 JOB 643531

[Diya Yang]

Hi there,

My FUMA SNP2GENE kept failing and I cannot figure out the problem. My summary stats is emailed to you guys. Could you please help look into this at your earliest advance?

Thank you so much!

Best,

Diya

[Tanya Phung]

Hi Diya,

I found this in your input file: 

awk '$2==11{print}' eGFR_CKDGEN_UKBB_MVP_EUR_noMHC_b37_FUMA_final.txt | grep NA
rs34287067      11      47757631        NA      NA      0.0000000000    0.0021157900    0.008491        223386

While for the other rows: 
head -n 3 eGFR_CKDGEN_UKBB_MVP_EUR_noMHC_b37_FUMA_final.txt
SNP     CHR     BP      A1      A2      BETA    SE      P       N
rs17244250      9       139818770       C       G       0.0002449400    0.0010983800    0.8239  828879
rs7860304       9       139819398       C       T       0.0009126940    0.0010826700    0.3994  853109

FUMA expects the 4th column to have the A1 allele and the 5th column to have the A2 allele. NA is not an acceptable alleles. 

Please see a similar response here for more information: https://groups.google.com/g/fuma-gwas-users/c/rtTZRBLC8g8/m/eOD0CCy5AwAJ

You can either remove the problematic row (or rows - you need to double-check) or fill in the alleles for the missing ones. 

Best,
Tanya