can any one say how to write script in plink having only individual ID and genotype data, I am not having family ID, parental ID, sex and phenotype.
Add --no-fid, --no-parents, --no-sex, and --no-pheno to your plink command line.
hello sir, actually i am having SNP data in hapmap format generated by GBS (crop=maize), i converted the hap to .ped and .map format. the ped form as usually has six column with missing FID,parents, SEX, phenotype. In these regard when i tried calculate allel frequency on chromosome wise, the out put says scaning 0 of 0 chr. (maize chr no is 10)
ex : ERROR: Problem with MAP file line:
1 S1523360 0 523360
2. here the phenotyping data is taken from field for quantitative traits, how can go for case/control for data. has there is no controls. suggest me the input format or command line for this situation
your reply could help me a lot