rvtests icon indicating copy to clipboard operation
rvtests copied to clipboard

Published 20 hours ago • verified publisher icon zhanxw

Output specification

Open bibb opened this issue 6 years ago • 8 comments

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

bibb avatar Dec 08 '17 22:12 bibb

This is something I'd also like to know.

ftlin22 avatar Feb 06 '18 16:02 ftlin22

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

dkainer avatar Mar 05 '18 20:03 dkainer

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

MiltonKoB avatar Nov 06 '18 17:11 MiltonKoB

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

learb avatar Nov 14 '18 16:11 learb

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/

zx8754 avatar Feb 06 '19 07:02 zx8754

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

jeong2624 avatar Sep 02 '20 02:09 jeong2624

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.

Galadrielf avatar Apr 27 '22 11:04 Galadrielf

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

katyaorlova avatar Oct 14 '22 18:10 katyaorlova