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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Problem with N_INFORMATIVE after --impute drop #60

Open BEFH opened 6 years ago

BEFH commented 6 years ago

I run the following, expecting missing genotypes to be dropped for any given variant:

./rvtest --inVcf [file] --impute drop --pheno [pheno file] --pheno-name [pheno] \
--sex --covar [pheno file] --covar-name [list,of,phenos] --out [out file stem] \
--single score,wald

The following is in the log: [INFO] Drop missing genotypes

However, the N_INFORMATIVE column in the association file is always the total N of my cohort, not the number of variants with genotype for each variant. Is this a reporting issue, or is RVTESTS failing to drop missing genotypes.

zhanxw commented 5 years ago

Looks like a bug. Let me check.