Case-Control Discrimination In .Ped File Of Plink

Question

[mandar.bobade60]

Hi,

I have two queries:

1) I have .ped file (mentioned below). Here, I have all columns required for GWAS. But I have this data-set where I am not able to understand how to descriminate between case and control or more precisely which column indicates case and control information?

2) If I don't have case-control descrimination, will I be able to perform GWAS. If yes, can u please suggest me links which I should follow for same.

Genotype file:

1 DVDAC003 0 0 0 0 A G T T A A C G C G A C A C A A C G A G G G C G G G A G C C G G G G G G 0 0 0 0 0 0 0 0 0 0 0

2 DVDAP001 0 0 0 0 A G T T A A G G C G A A C C A G G G A A G G C C G G A G C C A G A G G G 0 0 0 0 0 0 0 0 0 0 0

3 DVDAP003 0 0 0 0 A G T T A A C C G G C C A C G G C G G G A A G G G G A G C C G G A A G G 0 0 0 0 0 0 0 0 0 0 0

4 DVDAP004 0 0 0 0 G G T T A A C G C G A A C C A G C G A G G G G G G G G G C C G G A G G G 0 0 0 0 0 0 0 0 0 0 0

5 DVDAP006 0 0 0 0 G G A T A G C G C G A A C C A G C C A A A G G G G G G C C G G A G G G 0 0 0 0 0 0 0 0 0 0 0 0

Answer 1

[chrchang523]

Case/control status is normally coded as 1s and 2s in the sixth column of the .ped file. Occasionally it is coded as 0/1, in which case you need to use the --1 flag to get PLINK to interpret the column correctly.

If you don't see ANY 1s in the sixth column, then you'll have to ask your collaborator to provide you another file with case/control status. (This second file can then be loaded with --pheno.) You cannot perform GWAS without phenotype data.