Question: what is file format for phenotype file for SNPTEST?
0
gravatar for anamaria
15 months ago by
anamaria100
anamaria100 wrote:

Hello,

I was trying to run SNPTEST but I got this error:

Phenotype summary :
!! Error in function: CohortIndividualSource::ColumnSpec::find_column(), argument(s): column_name="anamaria/convert/LASER.ped".
.
!! Quitting.
!! Error (HaltProgramWithReturnCode)

My phenotype file looks like this:

1       K05914  0       0       2       1
2       K06757  0       0       1       2
3       K06768  0       0       1       1
4       K07479  0       0       2       1

Does someone know what SNPTEST expects in this pehnotype file?

I intend to run it like this:

./snptest \
-data ./example/cohort1.gen ./example/cohort1.sample \
-o ./example/ex.out \
-method score \
-frequentist 1 \
-pheno pheno1

Thanks Ana

snptest • 458 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by anamaria100
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