Entering edit mode
7.9 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 --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?
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.