Hi all,
I called SNPs from mRNA data of two tissues of Brassica napus. Among 320 genotypes, I wrongly sequence one genotype two times by giving two different names (a and c). Problem is my genotypic data exceed than phenotypic data (in genotypic numbers). I tried many times to cut that one genotypic data or column using the Linux command line. But, after the cut, either there is space error due to the cut of that column or disturb headers. So I can't run plink properly if run plink successfully then, later on, .tfam file generated from emmax command for kinship could not read columns after that particular column (that I cut in the original file). Finally, I can't do GWAS analysis properly. On the other hand, if I not cut the wrong column and add the same phenotypic values (because genotypic numbers are equal) twice then I can run all analyses from plink to GWAS.
My question is either can you please tell me the correct Linux command (as I tried several but not successful they way I want) or please guide me if I use phenotypic values for one genotype two times then what will overall effect on the quality of my GWAS data. If no difference then I can do this way. Thanks!
If you want help, you will have to show some example input and desired output.