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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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results for cmcWald #85

Closed apampana closed 4 years ago

apampana commented 5 years ago

I am running cmcWald on single gene and i am getting multiple same variants as output with different pvalues. Is it some kind of bug? Its happening only with cmcWALD? image

apampana commented 5 years ago

here is my code. /medpop/esp2/akhil/topmed/mend_genes/vcf_fh/executable/rvtest --inVcf name.vcf.gz --setFile try.set --pheno try.ped --pheno-name ldladj --qtl --covar-name age,sex,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,ever_smoked --out ldlr --burden cmcWald --freqUpper 0.01

apampana commented 5 years ago

can u help me with this? Thank you

zhanxw commented 4 years ago

That is the estimations for different covariates (e.g., variant X:110688592, age, sex, PC1, ...) .