Hello there,

I would greatly appreciate any help with this, and I apologise if it is really simple.

I am trying to use the --make-pheno command in plink to convert my phenotype text file to a phenotype file so that I can use this in subsequent analysis

The format of the phenotype.txt at present is in a unix txt tab delimited file The first few lines are as follows:

FID IID MN  p_pos   s_pos   a_pos
MN001CORCON MN001CORCON 2   -9  -9  -9
MNBEL02013012015P   MNBEL02013012015P   2   1   1   -9
MNBRA01102082014P   MNBRA01102082014P   2   2   1   -9
MNCAM0051922014PMP  MNCAM0051922014PMP  2   1   1   -9

I have also tried converting column 3 to the default of * to signify case However I keep coming up with errors I have tried entering the value for cases in quotation marks like '*' which has not worked

The command I am entering is:

plink2 --make-pheno phenotype.txt '2'

My output is: Options in effect: --make-pheno mnpppht2.txt 2

Error: No input dataset.

I have also tried this:

plink --bfile filename --make-pheno phenotype.txt 2 --make-bed --out newfilename

But got this error for the phenotype data from - output: --make-pheno: 0 phenotype values set.

Any help would be very much appreciated as I need to have a functioning phenotype file in order to do further data analysis.

Thank you very much Sanjana