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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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"unparsed option" when trying to use *bgen file in version 20171010 #41

Closed cerulean10 closed 5 years ago

cerulean10 commented 6 years ago

Hello,

 Based on comments in thread 38,  I am using the 20171010 rvtest version with a viable *bgen file and phenotype file in *ped format (NOT using sample file as was stated these are not supported yet).

However the program does not seem to recognize the --inBgen flag, please advise. Relevant output is as follows:

Effective Options --out test1000_bgen_gp.out --covar EA.cov --covar-name age,pc1,pc2,pc3 --sex --pheno EA.ped --pheno-name EA --dosage GP --meta score --impute drop --noweb

Unparsed arguments: --inBgen testrv1000_GP.bgen

best regards, Polly

zhanxw commented 5 years ago

Please use the latest version. It support the --inBgen option. Thanks.