Output specification - Githubissues

zhanxw / rvtests

Rare variant test software for next generation sequencing data

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Output specification #50

Open bibb opened 6 years ago

bibb commented 6 years ago

Hello,

This could sound silly, but could you please provide a detailed description about each column in the output files?, I have read all the documentation but I couldn't find anything for the output coming from CMC, SKAT, etc... there is only explanation for the meta-analysis output. For example, what does NumPolyVar means in the burden CMC output?

Thank you

ftlin22 commented 6 years ago

This is something I'd also like to know.

dkainer commented 6 years ago

yes, i also would like to see this documented. Thanks for this excellent software

MiltonKoB commented 5 years ago

Would highly appreciate, even very simple description for each column. Thanks for the superb software.

learb commented 5 years ago

+1 on this request, and again really great software :smile:

zx8754 commented 5 years ago

Yes, please, we need this.

After searching the repo, this is what it looks like it means:

NumPolyVar - number of Polymorphic Genotypes

buf.updateValue("NumPolyVar", dc.getFlippedToMinorPolymorphicGenotype().cols);

Related Q&A at BioStars:

https://www.biostars.org/p/279635/

jeong2624 commented 4 years ago

I want to know what is ActualPerm in VT test output. Also, what do NumGreater and NumEqual mean in VT test output?

Galadrielf commented 2 years ago

Hello, I am also here to ask the definitions of columns in the outputs of tests. Is there any update/source regarding this question? Because I could not find it. Thank you in advance.

katyaorlova commented 1 year ago

Still nothing on the internet in late 2022 about the column names for CMC and SKAT output beyond NumVar, NumPolyVar and NonRefSite?