Question: Plink input format
gravatar for dinesh
3.4 years ago by
dinesh50 wrote:


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. 


snp tutorial • 1.2k views
ADD COMMENTlink modified 3.4 years ago by chrchang5233.7k • written 3.4 years ago by dinesh50
gravatar for chrchang523
3.4 years ago by
United States
chrchang5233.7k wrote:

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

ADD COMMENTlink written 3.4 years ago by chrchang5233.7k

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

ADD REPLYlink written 3.4 years ago by dinesh50
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