Allele frequency and covariate outputs about rvtests HOT 4 CLOSED

Hello Carolina,

When you use "--meta score", the allele frequency is outputted.
Did you use that option?

The covariates outputs are automatically hidden, as RVTESTS performs score tests.

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Dear Zhan I am sorry if I confused you but I am runing a single variant analysis so my command is to this end

../executable/rvtest --pheno pheno --inVcf example.vcf --single wald --out out1

And this command does not output does not report frequency, here the header

CHROM POS REF ALT N_INFORMATIVE Test Beta SE Pvalue

By using
../executable/rvtest --pheno pheno --inVcf example.vcf --single wald --covar covar --covar-name c1,c2 --out out4

I get association results for all covariates (in my case 20 PCs for which I do not need the output and increase dramatically the size of my file... thats the reason I wanted to know if it is possible to have the option "--hide-covar" and get only the SNP association.

I hope now I have been clear. Best regards, Carolina

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thanks!

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Hello,
Regarding the --hide-covar flag, it seems as though it doesn't work when combined with trying to run the cmc Wald test? I've tried with and without the flag, but the output stays consistent (reporting one with all covariates accounted for, and one p-value per covariate as well)

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