8 Covariates

It is possible to perform the AI test with a set of covariates. To do this use the -covar option. For example:

./snipsnip -covar covariates.dat -o myresults.dat mydata.bed

The format of the covariate file is the same as PLINK covariate files. That is, a text file where the first column is the pedigree ID, the second column is the individual ID and the remaining columns are the covariate values, where a value of -9 denotes a missing value (this may be changed with the -mqtv option). For example, a covariate file with 3 covariates may look as follows:

PEDID ID SMOKE ALCOHOL EX 
WXA_T1233 WXA_T120 0.0037 0.0033 0.0207
WXA_T1233 WXA_T121 -0.0019 0.022 0.0257
WXA_T1234 WXA_T987 0.0104 0.0096 -0.0154
...

The header line may be present or not. The covariates may be chosen with the header names as follows:

./snipsnip -covar covariates.dat -covar-name ALCOHOL,EX -o myresults.dat mydata.bed

or

./snipsnip -covar covariates.dat -covar-name ALCOHOL-EX -o myresults.dat mydata.bed

to include all covariates between and including these two. Note that no spaces should be used between the chosen covariate values. The covariates may also be chosen by their numbers. So the above may be written:

./snipsnip -covar covariates.dat -covar-number 2,3 -o myresults.dat mydata.bed

or

./snipsnip -covar covariates.dat -covar-number 2-3 -o myresults.dat mydata.bed