Question: PLINK : Error: --tdt requires a case/control phenotype.
0
gravatar for bsmith030465
9 months ago by
bsmith030465150
United States
bsmith030465150 wrote:

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?

plink • 226 views
ADD COMMENTlink modified 9 months ago by chrchang5236.9k • written 9 months ago by bsmith030465150
3
gravatar for chrchang523
9 months ago by
chrchang5236.9k
United States
chrchang5236.9k wrote:

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.

ADD COMMENTlink written 9 months ago by chrchang5236.9k

Ah, my mistake!! Thanks, that worked!

ADD REPLYlink written 9 months ago by bsmith030465150
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