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/test-data/rgtestouts/rgQC/tinywga.log

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 48 lines | 40 code | 8 blank | 0 comment | 0 complexity | d0a5a02c20b4509ed0dc6a61860d3dcb MD5 | raw file
 1
 2@----------------------------------------------------------@
 3|        PLINK!       |     v1.06      |   24/Apr/2009     |
 4|----------------------------------------------------------|
 5|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
 6|----------------------------------------------------------|
 7|  For documentation, citation & bug-report instructions:  |
 8|        http://pngu.mgh.harvard.edu/purcell/plink/        |
 9@----------------------------------------------------------@
10
11Skipping web check... [ --noweb ] 
12Writing this text to log file [ tinywga.log ]
13Analysis started: Wed May 19 15:15:38 2010
14
15Options in effect:
16	--noweb
17	--bfile ldp_tinywga
18	--het
19	--out tinywga
20
21Reading map (extended format) from [ ldp_tinywga.bim ] 
2214 markers to be included from [ ldp_tinywga.bim ]
23Reading pedigree information from [ ldp_tinywga.fam ] 
2440 individuals read from [ ldp_tinywga.fam ] 
2540 individuals with nonmissing phenotypes
26Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
27Missing phenotype value is also -9
2810 cases, 30 controls and 0 missing
2921 males, 19 females, and 0 of unspecified sex
30Reading genotype bitfile from [ ldp_tinywga.bed ] 
31Detected that binary PED file is v1.00 SNP-major mode
32Before frequency and genotyping pruning, there are 14 SNPs
3327 founders and 13 non-founders found
34Total genotyping rate in remaining individuals is 0.991071
350 SNPs failed missingness test ( GENO > 1 )
360 SNPs failed frequency test ( MAF < 0 )
37After frequency and genotyping pruning, there are 14 SNPs
38After filtering, 10 cases, 30 controls and 0 missing
39After filtering, 21 males, 19 females, and 0 of unspecified sex
40
41 **Warning** this analysis typically requires whole-genome level data
42             to give accurate results 
43
44Converting data to Individual-major format
45Writing individual heterozygosity information to [ tinywga.het ] 
46
47Analysis finished: Wed May 19 15:15:38 2010
48