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zhanxw
Using --sex as covariate
Just to be sure, if I use the same .txt file (tab delimited, with correct column headers etc.) as the phenotype file and covariate file, do I use --sex (which is my 5th column header in the txt.) or do I include the ,sex, column in the --covar-name argument, or does this not matter at all?
Edit: I've ran a few GWASs using this setup (both with --sex and with ,sex, amongst --covar-name) and none gave an error, I'm just not sure about the specifics on whether it would matter.
I think in the "comments" first lines of your results you will see a summary of the model you ran, there you can check
##Covariates=age,age2,c1,c2,c3,c4,c5,c6,c7,c8,c9,C10 ##CovariateSummary min 25th median 75th max mean variance ##age 59 67 73 79 101 73.6604 69.4819 ##age2 3481 4489 5329 6241 10201 5495.29 1.58549e+06 ##c1 -0.0139819 -0.0024291 -6.43993e-06 0.00240237 0.110959 0.000241323 3.72289e-05 ##c2 -0.102322 -0.00205314 0.00010436 0.00216791 0.072016 2.94936e-05 3.29371e-05 ##c3 -0.0695761 -0.0021796 5.45516e-05 0.00241793 0.0822871 0.000202628 3.37562e-05 ##c4 -0.0525821 -0.00235731 1.85177e-05 0.0021723 0.108952 0.000138893 3.42132e-05 ##c5 -0.0149906 -0.00234976 -0.000218209 0.00190186 0.057528 -4.71888e-05 2.04726e-05 ##c6 -0.0901247 -0.00243602 -1.42429e-05 0.00218675 0.08763 -7.65006e-05 4.14908e-05 ##c7 -0.098898 -0.00228903 -0.00010105 0.00233804 0.0568693 -0.000167825 3.5344e-05 ##c8 -0.0853129 -0.00241098 7.71192e-06 0.00245196 0.0358697 -0.000217961 3.09375e-05 ##c9 -0.108387 -0.00246544 0.00022328 0.00278242 0.0263637 -3.94721e-05 3.43715e-05 ##C10 -0.0880471 -0.00266803 -8.48143e-05 0.00239904 0.0498765 -0.000135721 3.14865e-05 ##NullModelEstimates
