/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. 

  2. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    3. 

  3. |----------------------------------------------------------|
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  4. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    5. 

  5. |----------------------------------------------------------|
    6. 

  6. |  For documentation, citation & bug-report instructions:  |
    7. 

  7. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
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  8. @----------------------------------------------------------@
    9. 

  9. 

  10. Skipping web check... [ --noweb ] 
    11. 

  11. Writing this text to log file [ tinywga.log ]
    12. 

  12. Analysis started: Wed May 19 15:15:38 2010
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  13. 

  14. Options in effect:
    15. 

  15. 	--noweb
    16. 

  16. 	--bfile ldp_tinywga
    17. 

  17. 	--het
    18. 

  18. 	--out tinywga
    19. 

  19. 

  20. Reading map (extended format) from [ ldp_tinywga.bim ] 
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  21. 14 markers to be included from [ ldp_tinywga.bim ]
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  22. Reading pedigree information from [ ldp_tinywga.fam ] 
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  23. 40 individuals read from [ ldp_tinywga.fam ] 
    24. 

  24. 40 individuals with nonmissing phenotypes
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  25. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
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  26. Missing phenotype value is also -9
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  27. 10 cases, 30 controls and 0 missing
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  28. 21 males, 19 females, and 0 of unspecified sex
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  29. Reading genotype bitfile from [ ldp_tinywga.bed ] 
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  30. Detected that binary PED file is v1.00 SNP-major mode
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  31. Before frequency and genotyping pruning, there are 14 SNPs
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  32. 27 founders and 13 non-founders found
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  33. Total genotyping rate in remaining individuals is 0.991071
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  34. 0 SNPs failed missingness test ( GENO > 1 )
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  35. 0 SNPs failed frequency test ( MAF < 0 )
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  36. After frequency and genotyping pruning, there are 14 SNPs
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  37. After filtering, 10 cases, 30 controls and 0 missing
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  38. After filtering, 21 males, 19 females, and 0 of unspecified sex
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  39. 

  40.  **Warning** this analysis typically requires whole-genome level data
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  41.              to give accurate results 
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  42. 

  43. Converting data to Individual-major format
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  44. Writing individual heterozygosity information to [ tinywga.het ] 
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  45. 

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