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weizhouUMICH / SAIGE

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ERROR: SNP has B = 16 (not 8) #45

Closed FloWuenne closed 6 years ago

FloWuenne commented 6 years ago

Hi there,

I am trying to run SAIGE on a binary trait from the UKBB and I wanted to test a small subset of SNPs before running all chromosomes. I am running SAIGE_0.29.3.

I fitted the model using the 93 511 SNPs from the kinship calculations, as you did in the SAIGE manuscript for 424772 samples. My model was fitted using Sex, Age, PC1, PC2, PC3, PC4 as non genetic covariates. I am trying to run SAIGE on 10 markers on chromsome 22. The bgen file contains genotype calls for all samples and only the 10 markers to be tested.

I get the following error when trying to run step2 of SAIGE:

Minimum MAF of markers to be testd is  1e-04 
Analysis started at  1.54e+09 Seconds
no query list is provided
424772 samples are found in the bgen file
10 markers are found in the bgen file 
isVariant:  TRUE 
It is a binary trait
Analyzing  8381  cases and  416391  controls 
ERROR: rs9628178 has B = 16 (not 8)

Could you please help me out to find the cause of this specific error?

FloWuenne commented 6 years ago

I just found another issue that tackles the same problem that I overlooked when going through the issues the first time. This issue can be closed.

Users with the same problem please refer to #22 !