root/galaxy-central/test-data/rgtestouts/rgQC/tinywga.log

@----------------------------------------------------------@
|        PLINK!       |     v1.06      |   24/Apr/2009     |
|----------------------------------------------------------|
|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ tinywga.log ]
Analysis started: Wed May 19 15:15:38 2010

Options in effect:
        --noweb
        --bfile ldp_tinywga
        --het
        --out tinywga

Reading map (extended format) from [ ldp_tinywga.bim ] 
14 markers to be included from [ ldp_tinywga.bim ]
Reading pedigree information from [ ldp_tinywga.fam ] 
40 individuals read from [ ldp_tinywga.fam ] 
40 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
10 cases, 30 controls and 0 missing
21 males, 19 females, and 0 of unspecified sex
Reading genotype bitfile from [ ldp_tinywga.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 14 SNPs
27 founders and 13 non-founders found
Total genotyping rate in remaining individuals is 0.991071
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 14 SNPs
After filtering, 10 cases, 30 controls and 0 missing
After filtering, 21 males, 19 females, and 0 of unspecified sex

 **Warning** this analysis typically requires whole-genome level data
             to give accurate results 

Converting data to Individual-major format
Writing individual heterozygosity information to [ tinywga.het ] 

Analysis finished: Wed May 19 15:15:38 2010