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?