PLINK input files from Genome Studio

Question

[matziast]

Hi, I am new in PLINK and Genome Studio and I apologize for my question. I have raw data from sequencing in Genome Studio and I want to create input files for PLINK. I used PLINK plugin of Genome Studio and everything was ok. When I load the files in PLINK, all the phenotypes were missing. Could anyone help me? Thank you in advance.

267607 (of 267607) markers to be included from [ GREEK_PD_GWAS_NEW_6213.map ]
Warning, found 36 individuals with ambiguous sex codes
These individuals will be set to missing ( or use --allow-no-sex )
Writing list of these individuals to [ plink.nosex ]
2151 individuals read from [ GREEK_PD_GWAS_NEW_6213.ped ] 
0 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
0 cases, 0 controls and 2151 missing
1160 males, 955 females, and 36 of unspecified sex
Before frequency and genotyping pruning, there are 267607 SNPs
2151 founders and 0 non-founders found
48968 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ plink.hh ]
664 SNPs with no founder genotypes observed
Warning, MAF set to 0 for these SNPs (see --nonfounders)
Writing list of these SNPs to [ plink.nof ]
Total genotyping rate in remaining individuals is 0.993605
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 267607 SNPs
After filtering, 0 cases, 0 controls and 2151 missing
After filtering, 1160 males, 955 females, and 36 of unspecified sex

[chrchang523]

Did you ever provide any phenotype information? If so, how?

Answer 1

[matziast]

Hi, Thank you for your reply. I only used plugin of Genome Studio for PLINK regarding a file with.bsc extension. The column in file.fam was -9 for all subjects. I do not know the reason.