PLINK : Error: --tdt requires a case/control phenotype.

Question

[bsmith030465]

Hi,

I was trying to run an analysis:

plink --bfile my.samples --tdt

but get the following error:

Error: --tdt requires a case/control phenotype.

The corresponding family file seems to be okay (i.e. case/control status looks ok):

MJ19    ID55  ID57  ID56  2   2
MJ19    ID56  0   0   2   1
MJ19    ID57  0   0   1   1
MJ23    ID67  ID69  ID68  1   2
MJ23    ID68  0   0   2   1
MJ23    ID69  0   0   1   1
.
.

plink version: PLINK v1.90b6.10 64-bit (17 Jun 2019)

Is there anything else that I need to set?

thanks!

EDIT: I made the bed (from ped) file with the following command:

plink --file my.samples --make-bed --out my.samples --missing-genotype N

I just noticed that the log file has:

8973 variants and 316 people pass filters and QC.
Phenotype data is quantitative.

Shouldn't this be affectation status and not quantitative?

Answer 1

[chrchang523]

The first six lines are okay, but plink has told you that at least one of the other 310 lines is not okay. Find and fix the problem.

[bsmith030465]

Ah, my mistake!! Thanks, that worked!