Entering edit mode
8.6 years ago
afadda ▴ 20


I'm running the following command to find runs of homozygosity:

plink --bfile path/G02 --homozyg --out path/G02 --allow-no-sex

I get this log:

Writing this text to log file [ path/G02.log ]
Analysis started: Sun May  3 14:16:01 2015

Options in effect:
    --bfile path/G02
    --out path/G02

Reading map (extended format) from [path/G02.bim ]
3923914 markers to be included from [ path/G02.bim ]
Reading pedigree information from [ path/G02.fam ] 
1 individuals read from [ path/G02.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 1 missing
0 males, 0 females, and 1 of unspecified sex
Warning, found 1 individuals with ambiguous sex codes
Writing list of these individuals to [ path/G02.nosex ]
Reading genotype bitfile from [ path/G02.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 3923914 SNPs
1 founders and 0 non-founders found
Total genotyping rate in remaining individuals is nan
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 3923914 SNPs
After filtering, 0 cases, 0 controls and 1 missing
After filtering, 0 males, 0 females, and 1 of unspecified sex
Converting data to Individual-major format

Writing homozygosity-run information to [ path/G02.hom ] 
Run defined as: 
Homozygous segment criteria:
  length (kb)       = 1000
  # SNPs (N)        = 100
  density (kb/SNP)  = 50
  largest gap (kb)  = 1000
1 of 1 individuals      

Writing segment summary to [path/G02.hom.indiv ]
Writing segment summary to [ path/G02.hom.summary ]

I get nothing in the homo files except the headings. Anyone has any idea on why this is?


plink ROH • 7.9k views
Entering edit mode

In .ped file, if you don't have information for family ID, paternal, maternal and sex ID, then specified "0" instead -9. It would solve your problem.


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