assigning cases and controls in plink

Question

[nchuang]

Quick question.

I am trying to assign cases in my study for association test with --make-pheno cases.list '*' option but program keeps telling me there's less than two phenotypes. My command line is:

plink --bfile cases --make-pheno cases.list '*' --assoc

My cases.list file has two columns with FID and IID like this:

18175   1
19233   1
19302   1
19342   1
19367   1
19427   1
19477   1

I am using plink 1.9

Answer 1

[Vanya]

plink --bfile cases --pheno casefilename.txt --make-bed --out newfilename

Above command is to update phenotype of cases which is coded by digit 2as explained below e.g.

18175   2
19233   2
19302   2
19342   2
19367   2
19427   2
19477      2

but if you wish to perform association testing(--assoc) you must include control samples as well along with the cases.