rgcgithub/regenie

empty output file

Opened this issue · 1 comments

lcmajara commented

Hi,

For some seemingly un-obvious reason, regenie removes all variants from association test.
Specifically, the Number of ignored tests due to low MAC is exactly the same number of variants in the input file.
I've computed the mac for the variants, and there are millions of variants with mac > 5 (the default threshold)

I've running the code as below:
regenie --step 1
--force-step1
--bed {plink_file}
--phenoFile {pheno_file}
--phenoCol
super_pheno
--covarFile {pheno_file}
--covarColList PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,sex,age
--extract {snplist}
--bsize 1000
--verbose
--bt
--out {s}-{pheno}

regenie --step 2
--bed {plink_file}
--phenoFile {pheno_file}
--phenoCol super_pheno
--covarFile {pheno_file}
--catCovarList sex
--pred {s}-{pheno}_pred.list
--bsize 1000
--verbose
--af-cc
--bt
--gz
--out {s}-{pheno}

I'm not sure why this would be happening. Please help.

joellembatchou commented