PLINK : Problem with .assoc file

Question

[cdg]

I have a problem with my .assoc file that is created after : ./plink --noweb --ped ../OUTPUT.cases.ped --map ../OUTPUT.cases.map --maf 0.05 --assoc --out Qcases . When i open the Qcases.assoc file , the columns F_A , F_U , CHISQ , P , OR has value NA but it was supposed to have a number (as if i run the same command for the default test that PLINK has it calculate all values above).. I've searched for more arguments but I cannot find anything. Any Help?

[Sam]

Seems like you are using plink 1.7, what's the log? Generally, it is advised to provide the log to the program output so that we can figure out what's going on.

And what happen if you use plink1.9 https://www.cog-genomics.org/plink2/

[cdg]

This is the output of the command and i thought if maybe the missing phenotype is the problem(as it says) . The .haps , .gen , .sample files were created by hapgen2 and with GTOOL i converted them to .map and .ped. My files are : .ped , .haps , .sample , .map and .ped .

For Data i used chromosome 6 from Hapgens hapmap 3 . Here are my specifis commands (if they help) :

Hapgen2

• ./hapgen2 -h hapmap3_r2_b36/hapmap3_r2_b36_chr6.haps -l hapmap3_r2_b36/hapmap3_r2_b36_chr6.legend -m hapmap3_r2_b36/genetic_map_chr6_combined_b36.txt -o OUTPUT -dl 2359212 1 2 2.5 -n 100 100

GTOOL

• ./gtool -G --g OUTPUT.cases.gen --s OUTPUT.cases.sample --ped OUTPUT.cases.ped --map OUTPUT.cases.map --threshold 0.9
• ./gtool -G --g OUTPUT.controls.gen --s OUTPUT.controls.sample --ped OUTPUT.controls.ped --map OUTPUT.controls.map --threshold 0.9

PLINK

• ./plink --noweb --ped ../OUTPUT.cases.ped --map ../OUTPUT.cases.map --maf 0.05 --assoc --out QQcases

Answer 1

[Sam]

Your ped file doesn't contain any phenotype (the sixth column), therefore you cannot perform the association analysis. In addition, as your ped file also doesn't contain any sex information, you might need to add --allow-no-sex in order to perform the association (as sample without sex information is ignored for association analysis)