Hi! I have a Plink gwas data set. All files are in binary format (.bed,.bim).
Before I get into details, here is my question: How can I subset for subjects I am interested in using Plink?
I am aiming to subset a group of individuals for my analysis, however when I run the following command my plink log file has the following output. I'm also including what the include subjects file looks like as well:
plink --bfile /path/to/plink/files --keep /path/to/includesubjects.txt --make-bed --out /path/to/subsetted/plink/files
EXAMPLE OF TEXT FILE WITH INDIVIDUALS I WANT TO INCLUDE: The '0' correspond to the fam ID. These are unrelated subjects so I did not include a family ID. This also corresponds to what is in the fam file.
0 Subject_001 0 Subject_002 0 Subject_003 0 Subject_004 0 Subject_005 0 Subject_006
PLINK OUTPUT: Writing this text to log file [ /path/to/log/file.log ] Analysis started: Wed Apr 19 15:36:22 2017
Options in effect: --bfile /path/to/plink/files --keep /path/to/includesubjects.txt --make-bed --out /path/to/subsetted/plink/files Reading map (extended format) from [ /path/to/plink/files.bim ] 5 markers to be included from [ /path/to/plink/files.bim ] Reading pedigree information from [ /path/to/plink/files.fam ] 940 individuals read from [ /path/to/plink/files.fam ] 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 940 missing 559 males, 381 females, and 0 of unspecified sex Reading genotype bitfile from [ /path/to/plink/files.bed ] Detected that binary PED file is v1.00 SNP-major mode Reading individuals to keep [ path/to/includesubjects.txt ] ... 0 read 940 individuals removed with --keep option Before frequency and genotyping pruning, there are 5 SNPs 0 founders and 0 non-founders found Total genotyping rate in remaining individuals is 0 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 5 SNPs