RVtests CMC output column definitions
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5.1 years ago
clyumath ▴ 20

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

next-gen SNP sequencing Rvtests • 3.2k views
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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?

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I contacted the developers by email, but no reply.

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Any luck receiving a reply?

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Having the same issue, ftlin22?

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unfortunately not yet.

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

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5.1 years ago

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.

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3.8 years ago
zx8754 11k

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

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