Plink input format

Question

[dinesh]

Hi,

Can anyone 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.

Answer 1

[chrchang523]

Add --no-fid, --no-parents, --no-sex, and --no-pheno to your plink command line.

[dinesh]

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 allele frequency on chromosome wise, the out put says scanning 0 of 0 chr. (maize chr no is 10)

ex:

ERROR: Problem with MAP file line:
           1    S1523360    0    523360

Here the phenotyping data is taken from field for quantitative traits, how can go for case/control for data as there is no controls. suggest me the input format or command line for this situation

Your reply could help me a lot