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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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AF reported as 0 for all variants with FamScore Test #34

Closed youngh11 closed 7 years ago

youngh11 commented 7 years ago

Hello,

My command is as follows: rvtest --inVcf vcf --pheno pheno --covar covariate --out out --kinship kinship.output.kinship --dosage DS --single FamScore

The AF column is 0 for all variants.

If the last flag is changed to --meta score, AF is reported. rvtest --inVcf vcf --pheno pheno --covar covariate --out out --kinship kinship.output.kinship --dosage DS --meta score

AF shows up and all other statistics are the same as with FamScore (p-value, ustat, etc).

Thank you!

zhanxw commented 7 years ago

I can confirm this problem. I will fix it.

zhanxw commented 7 years ago

Does this release fix your issue? https://github.com/zhanxw/rvtests/releases/tag/v2.0.5

youngh11 commented 7 years ago

That does fix the AF issue, thank you.