Question: ROH by PLINK
2
afadda • 20 wrote:
Hi,
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
--homozyg
--out path/G02
--allow-no-sex
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?
thanks!
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.