RVtests CMC output column definitions

Question

[clyumath]

When running CMC test, the output has NumVar, NumPolyVar, and NonRefSite. What do they mean?

• GitHub repo: https://github.com/zhanxw/rvtests
• Manual page: http://zhanxw.github.io/rvtests/

[bibb77]

Hello, I have the same question and I posted it in the github webpage (https://github.com/zhanxw/rvtests/issues/50) but no answer yet. Have you figured that out?

[clyumath]

I contacted the developers by email, but no reply.

[ftlin22]

Any luck receiving a reply?

[Kevin Blighe]

Having the same issue, ftlin22?

[clyumath]

unfortunately not yet.

[Louisa Pyle]

Did anyone get an answer to this? Having the same issue.

Answer 1

[raphael.B]

Late answer, but after checking, it is quite likely that numpolyvar corresponds to the number of variants use for association test, after discarding variants with null allele count in the study population. Num var appears to be the number of variants passing filters (frequency cutoff, etc).

Answer 2

[Kevin Blighe]

I would contact the developers in order to find out and to be sure: https://github.com/zhanxw/rvtests#feedbackcontact

It is not expressly stated what these output values represent.

Answer 3

[zx8754]

From searching their repo, they mean:

• NumVar: number of variants in the gene(or site)
• NumPolyVar: number of Polymorphic Genotypes
• NonRefSite: non-reference site, genotype is not exactly 0.0

Related GitHub issue #50