Document output format with `--htp` flag for region-based regenie step 2
Opened this issue · 5 comments
The output format for gene/region-based regenie step 2 [edit: when using --htp
] does not appear to be documented; https://rgcgithub.github.io/regenie/options/#output_1 just says it is "the same output format mentioned above."
With --build-mask sum
, [edit: as mentioned in #336, --htp
is intentionally ignored in this case, so] the columns have the same names as a single-variant run:
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA
but they are used in ways that don't quite match the header. Empirically, it looks like:
CHROM
andGENPOS
are the coordinates of the first variant in the regionID
is<gene name>.<mask name>
ALLELE0
is "ref"ALLELE1
is the mask nameA1FREQ
is presumably calculated after combining all alleles into a pseudo-allele as specified by--build-mask
(right?)TEST
is "ADD" (at least with all the input parameters I tried)EXTRA
is usually NA; presumably it's that "additional column included to specify if Firth/SPA corrections failed."- The rest of the columns are exactly what they say on the tin.
With [edit: --htp
and] --build-mask max
or --build-mask comphet
however, the output format is completely different, and now includes the following columns:
Name Chr Pos Ref Alt Trait Cohort Model Effect LCI_Effect UCI_Effect Pval AAF Num_Cases Cases_Ref Cases_Het Cases_Alt Num_Controls Controls_Ref Controls_Het Controls_Alt Info
As far as I can tell:
Name
is<gene name>.<mask name>
Chr
andPos
are again the coordinates of the first variantRef
is "ref"Alt
is the maskTrait
is the phenotype nameCohort
is "TEST"Model
is something like "ADD-WGR-FIRTH" (I get the gist but I'm not sure what the exact info conveyed here is?)- There are now columns for
Effect
,LCI_Effect
(?), andUCI_effect
(?) instead of a single beta Pval
is self-explanatoryAAF
I'm again assuming is calculated based on the combined pseudo-allelesNum_Cases
,Cases_Ref
, etc. are self-explanatory for binary traits, and for continuous traits the counts seem to be shoehorned in by considering everyone a "case" and leaving the "controls" columns NAInfo
seems to have a series of semicolon-separatedname=value
pairs, e.g.REGENIE_BETA=0.026852;REGENIE_SE=0.009518;MAC=160787.000000;SCORE=294.673996;SKATV=10948.247814;LOG10P=2.313457
I'd greatly appreciate if you could confirm or correct my assumptions here, fill in the gaps, and put all the information into the official documentation. A few "sample output" files could also be quite helpful, especially for designing workflows that take regenie's output as their input.
I'm guessing that LCI_Effect and UCI_Effect lower and upper ends confidence interface on the beta (aka Effect). Would be nice to have documentation of these.
@joellembatchou You are correct, we are using the --htp TEST
option. This particular regenie pipeline actually predates my tenure at my company, so I'll ask around and see if anyone else remembers why we did that.
My best guess here is that we specifically wanted the Cases_Ref / Cases_Het / Controls_Alt etc. statistics, which are not available in the standard, documented output format.
So I guess my request is for there to be some documented way to get the Cases_Ref / Cases_Het / Controls_Alt etc. statistics out of regenie: either document the currently-available --htp
, or add (an option for) these columns in the standard output format.