/test-data/rgtestouts/rgQC/rgQCtest1.html

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  6. <meta name="generator" content="Galaxy rgQC.py tool output - see http://g2.trac.bx.psu.edu/" />
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  11. <div class="document">
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  12. <h4>
    13. 

  13. <div>Output from Rgenetics QC report tool run at 19/05/2010 15:15:46<br>
    14. 

  14. </h4>
    15. 

  15. </div><div><h4>(Click any preview image to download a full sized PDF version)</h4><br><ol>
    16. 

  16. <table cellpadding="5" border="0">
    17. 

  17. <tr><td colspan="3"><a href="MarkerDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Marker QC Detail report file</a> (1.4 KB) tab delimited</td></tr>
    18. 

  18. <tr><td colspan="3"><a href="SubjectDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Subject QC Detail report file</a> (1.4 KB) tab delimited</td></tr>
    19. 

  19. <tr><td><a href="tinywga_All_Paged.pdf"><img src="tinywga_All_Paged-0.jpg" alt="All tinywga QC Plots joined into a single pdf" hspace="10" align="middle">
    20. 

  20. </a></td><td>All tinywga QC Plots joined into a single pdf</td><td>&nbsp;</td></tr>
    21. 

  21. <tr><td><a href="tinywga_All_3x3.pdf"><img src="tinywga_All_3x3-0.jpg" alt="All tinywga QC Plots 3 by 3 to a page" hspace="10" align="middle">
    22. 

  22. </a></td><td>All tinywga QC Plots 3 by 3 to a page</td><td>&nbsp;</td></tr>
    23. 

  23. <tr><td><a href="tinywga_logphweunaff.pdf"><img src="tinywga_logphweunaff.jpg" alt="Marker HWE" hspace="10" align="middle">
    24. 

  24. </a></td><td>Marker HWE</td><td><a href="Ranked_Marker_HWE.xls">Worst data</a></td></tr>
    25. 

  25. <tr><td><a href="tinywga_logphweunaff_cum.pdf"><img src="tinywga_logphweunaff_cum.jpg" alt="Ranked Marker HWE" hspace="10" align="middle">
    26. 

  26. </a></td><td>Ranked Marker HWE</td><td>&nbsp;</td></tr>
    27. 

  27. <tr><td><a href="QQtinywga_logphweunaff_cum.pdf"><img src="QQtinywga_logphweunaff_cum.jpg" alt="LogQQ plot Marker HWE" hspace="10" align="middle">
    28. 

  28. </a></td><td>LogQQ plot Marker HWE</td><td>&nbsp;</td></tr>
    29. 

  29. <tr><td><a href="tinywga_missfrac.pdf"><img src="tinywga_missfrac.jpg" alt="Marker Missing Genotype" hspace="10" align="middle">
    30. 

  30. </a></td><td>Marker Missing Genotype</td><td><a href="Ranked_Marker_Missing_Genotype.xls">Worst data</a></td></tr>
    31. 

  31. <tr><td><a href="tinywga_missfrac_cum.pdf"><img src="tinywga_missfrac_cum.jpg" alt="Ranked Marker Missing Genotype" hspace="10" align="middle">
    32. 

  32. </a></td><td>Ranked Marker Missing Genotype</td><td>&nbsp;</td></tr>
    33. 

  33. <tr><td><a href="tinywga_maf.pdf"><img src="tinywga_maf.jpg" alt="Marker MAF" hspace="10" align="middle">
    34. 

  34. </a></td><td>Marker MAF</td><td><a href="Ranked_Marker_MAF.xls">Worst data</a></td></tr>
    35. 

  35. <tr><td><a href="tinywga_maf_cum.pdf"><img src="tinywga_maf_cum.jpg" alt="Ranked Marker MAF" hspace="10" align="middle">
    36. 

  36. </a></td><td>Ranked Marker MAF</td><td>&nbsp;</td></tr>
    37. 

  37. <tr><td><a href="tinywga_fracmiss.pdf"><img src="tinywga_fracmiss.jpg" alt="Subject Missing Genotype" hspace="10" align="middle">
    38. 

  38. </a></td><td>Subject Missing Genotype</td><td><a href="Ranked_Subject_Missing_Genotype.xls">Worst data</a></td></tr>
    39. 

  39. <tr><td><a href="tinywga_fracmiss_cum.pdf"><img src="tinywga_fracmiss_cum.jpg" alt="Ranked Subject Missing Genotype" hspace="10" align="middle">
    40. 

  40. </a></td><td>Ranked Subject Missing Genotype</td><td>&nbsp;</td></tr>
    41. 

  41. <tr><td><a href="tinywga_s_het.pdf"><img src="tinywga_s_het.jpg" alt="Subject F Statistic" hspace="10" align="middle">
    42. 

  42. </a></td><td>Subject F Statistic</td><td>&nbsp;</td></tr>
    43. 

  43. <tr><td><a href="tinywga_s_het_cum.pdf"><img src="tinywga_s_het_cum.jpg" alt="Ranked Subject F Statistic" hspace="10" align="middle">
    44. 

  44. </a></td><td>Ranked Subject F Statistic</td><td>&nbsp;</td></tr>
    45. 

  45. <tr><td><a href="FQNormtinywga_s_het_cum.pdf"><img src="FQNormtinywga_s_het_cum.jpg" alt="F Statistic Subject F Statistic" hspace="10" align="middle">
    46. 

  46. </a></td><td>F Statistic Subject F Statistic</td><td>&nbsp;</td></tr>
    47. 

  47. </table><hr><h3>All output files from the QC run are available below</h3>
    48. 

  48. <table cellpadding="5" border="0">
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  49. 

  50. <tr><td><a href="FQNormtinywga_s_het_cum.jpg">FQNormtinywga_s_het_cum.jpg</a> (30.2 KB)</td></tr>
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  51. <tr><td><a href="FQNormtinywga_s_het_cum.pdf">FQNormtinywga_s_het_cum.pdf</a> (7.1 KB)</td></tr>
    52. 

  52. <tr><td><a href="MarkerDetails_rgQCtest1.xls">MarkerDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr>
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  53. <tr><td><a href="QQtinywga_logphweunaff_cum.jpg">QQtinywga_logphweunaff_cum.jpg</a> (33.0 KB)</td></tr>
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  54. <tr><td><a href="QQtinywga_logphweunaff_cum.pdf">QQtinywga_logphweunaff_cum.pdf</a> (6.6 KB)</td></tr>
    55. 

  55. <tr><td><a href="Ranked_Marker_HWE.xls">Ranked_Marker_HWE.xls</a> (763 B)</td></tr>
    56. 

  56. <tr><td><a href="Ranked_Marker_MAF.xls">Ranked_Marker_MAF.xls</a> (564 B)</td></tr>
    57. 

  57. <tr><td><a href="Ranked_Marker_Missing_Genotype.xls">Ranked_Marker_Missing_Genotype.xls</a> (659 B)</td></tr>
    58. 

  58. <tr><td><a href="Ranked_Subject_Missing_Genotype.xls">Ranked_Subject_Missing_Genotype.xls</a> (804 B)</td></tr>
    59. 

  59. <tr><td><a href="SubjectDetails_rgQCtest1.xls">SubjectDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr>
    60. 

  60. <tr><td><a href="ldp_tinywga.bed">ldp_tinywga.bed</a> (143 B)</td></tr>
    61. 

  61. <tr><td><a href="ldp_tinywga.bim">ldp_tinywga.bim</a> (392 B)</td></tr>
    62. 

  62. <tr><td><a href="ldp_tinywga.fam">ldp_tinywga.fam</a> (603 B)</td></tr>
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  63. <tr><td><a href="ldp_tinywga.log">ldp_tinywga.log</a> (2.0 KB)</td></tr>
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  64. <tr><td><a href="tinywga.fmendel">tinywga.fmendel</a> (378 B)</td></tr>
    65. 

  65. <tr><td><a href="tinywga.frq">tinywga.frq</a> (1.2 KB)</td></tr>
    66. 

  66. <tr><td><a href="tinywga.het">tinywga.het</a> (2.5 KB)</td></tr>
    67. 

  67. <tr><td><a href="tinywga.hwe">tinywga.hwe</a> (6.5 KB)</td></tr>
    68. 

  68. <tr><td><a href="tinywga.imendel">tinywga.imendel</a> (612 B)</td></tr>
    69. 

  69. <tr><td><a href="tinywga.imiss">tinywga.imiss</a> (1.9 KB)</td></tr>
    70. 

  70. <tr><td><a href="tinywga.lmendel">tinywga.lmendel</a> (571 B)</td></tr>
    71. 

  71. <tr><td><a href="tinywga.lmiss">tinywga.lmiss</a> (1.1 KB)</td></tr>
    72. 

  72. <tr><td><a href="tinywga.log">tinywga.log</a> (1.9 KB)</td></tr>
    73. 

  73. <tr><td><a href="tinywga.mendel">tinywga.mendel</a> (56 B)</td></tr>
    74. 

  74. <tr><td><a href="tinywga.prune.in">tinywga.prune.in</a> (140 B)</td></tr>
    75. 

  75. <tr><td><a href="tinywga.prune.out">tinywga.prune.out</a> (110 B)</td></tr>
    76. 

  76. <tr><td><a href="tinywga.sexcheck">tinywga.sexcheck</a> (2.5 KB)</td></tr>
    77. 

  77. <tr><td><a href="tinywga_All_3x3-0.jpg">tinywga_All_3x3-0.jpg</a> (45.2 KB)</td></tr>
    78. 

  78. <tr><td><a href="tinywga_All_3x3-1.jpg">tinywga_All_3x3-1.jpg</a> (19.3 KB)</td></tr>
    79. 

  79. <tr><td><a href="tinywga_All_3x3.pdf">tinywga_All_3x3.pdf</a> (82.4 KB)</td></tr>
    80. 

  80. <tr><td><a href="tinywga_All_Paged-0.jpg">tinywga_All_Paged-0.jpg</a> (13.6 KB)</td></tr>
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  81. <tr><td><a href="tinywga_All_Paged-1.jpg">tinywga_All_Paged-1.jpg</a> (26.3 KB)</td></tr>
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  82. <tr><td><a href="tinywga_All_Paged-10.jpg">tinywga_All_Paged-10.jpg</a> (31.4 KB)</td></tr>
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  83. <tr><td><a href="tinywga_All_Paged-11.jpg">tinywga_All_Paged-11.jpg</a> (29.8 KB)</td></tr>
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  84. <tr><td><a href="tinywga_All_Paged-2.jpg">tinywga_All_Paged-2.jpg</a> (32.3 KB)</td></tr>
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  85. <tr><td><a href="tinywga_All_Paged-3.jpg">tinywga_All_Paged-3.jpg</a> (11.1 KB)</td></tr>
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  86. <tr><td><a href="tinywga_All_Paged-4.jpg">tinywga_All_Paged-4.jpg</a> (26.7 KB)</td></tr>
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  87. <tr><td><a href="tinywga_All_Paged-5.jpg">tinywga_All_Paged-5.jpg</a> (18.4 KB)</td></tr>
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  88. <tr><td><a href="tinywga_All_Paged-6.jpg">tinywga_All_Paged-6.jpg</a> (28.1 KB)</td></tr>
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  89. <tr><td><a href="tinywga_All_Paged-7.jpg">tinywga_All_Paged-7.jpg</a> (11.9 KB)</td></tr>
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  90. <tr><td><a href="tinywga_All_Paged-8.jpg">tinywga_All_Paged-8.jpg</a> (29.6 KB)</td></tr>
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  91. <tr><td><a href="tinywga_All_Paged-9.jpg">tinywga_All_Paged-9.jpg</a> (17.9 KB)</td></tr>
    92. 

  92. <tr><td><a href="tinywga_All_Paged.pdf">tinywga_All_Paged.pdf</a> (81.9 KB)</td></tr>
    93. 

  93. <tr><td><a href="tinywga_fracmiss.jpg">tinywga_fracmiss.jpg</a> (12.0 KB)</td></tr>
    94. 

  94. <tr><td><a href="tinywga_fracmiss.pdf">tinywga_fracmiss.pdf</a> (6.4 KB)</td></tr>
    95. 

  95. <tr><td><a href="tinywga_fracmiss_cum.jpg">tinywga_fracmiss_cum.jpg</a> (30.0 KB)</td></tr>
    96. 

  96. <tr><td><a href="tinywga_fracmiss_cum.pdf">tinywga_fracmiss_cum.pdf</a> (7.0 KB)</td></tr>
    97. 

  97. <tr><td><a href="tinywga_logphweunaff.jpg">tinywga_logphweunaff.jpg</a> (13.6 KB)</td></tr>
    98. 

  98. <tr><td><a href="tinywga_logphweunaff.pdf">tinywga_logphweunaff.pdf</a> (5.7 KB)</td></tr>
    99. 

  99. <tr><td><a href="tinywga_logphweunaff_cum.jpg">tinywga_logphweunaff_cum.jpg</a> (26.8 KB)</td></tr>
    100. 

  100. <tr><td><a href="tinywga_logphweunaff_cum.pdf">tinywga_logphweunaff_cum.pdf</a> (5.8 KB)</td></tr>
    101. 

  101. <tr><td><a href="tinywga_maf.jpg">tinywga_maf.jpg</a> (18.5 KB)</td></tr>
    102. 

  102. <tr><td><a href="tinywga_maf.pdf">tinywga_maf.pdf</a> (6.4 KB)</td></tr>
    103. 

  103. <tr><td><a href="tinywga_maf_cum.jpg">tinywga_maf_cum.jpg</a> (28.5 KB)</td></tr>
    104. 

  104. <tr><td><a href="tinywga_maf_cum.pdf">tinywga_maf_cum.pdf</a> (6.0 KB)</td></tr>
    105. 

  105. <tr><td><a href="tinywga_missfrac.jpg">tinywga_missfrac.jpg</a> (11.1 KB)</td></tr>
    106. 

  106. <tr><td><a href="tinywga_missfrac.pdf">tinywga_missfrac.pdf</a> (5.9 KB)</td></tr>
    107. 

  107. <tr><td><a href="tinywga_missfrac_cum.jpg">tinywga_missfrac_cum.jpg</a> (27.3 KB)</td></tr>
    108. 

  108. <tr><td><a href="tinywga_missfrac_cum.pdf">tinywga_missfrac_cum.pdf</a> (5.9 KB)</td></tr>
    109. 

  109. <tr><td><a href="tinywga_s_het.jpg">tinywga_s_het.jpg</a> (18.0 KB)</td></tr>
    110. 

  110. <tr><td><a href="tinywga_s_het.pdf">tinywga_s_het.pdf</a> (6.8 KB)</td></tr>
    111. 

  111. <tr><td><a href="tinywga_s_het_cum.jpg">tinywga_s_het_cum.jpg</a> (31.9 KB)</td></tr>
    112. 

  112. <tr><td><a href="tinywga_s_het_cum.pdf">tinywga_s_het_cum.pdf</a> (7.3 KB)</td></tr>
    113. 

  113. </table><h4>QC run log contents</h4><pre>## subject reports starting at 19/05/2010 15:15:38
    114. 

  114. ## imissfile /opt/galaxy/test-data/rgtestouts/rgQC/tinywga.imiss contained 40 ids
    115. 

  115. ### writing /opt/galaxy/test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls report with ['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat']## marker reports starting at 19/05/2010 15:15:38
    116. 

  116. hwe header testpos=2,ppos=8,snppos=1
    117. 

  117. ## starting plotpage, newfpath=/opt/galaxy/test-data/rgtestouts/rgQC,m=[['snp', 'chromosome', 'offset', 'maf', 'a1', 'a2', 'missfrac', 'p_hwe_all', 'logp_hwe_all', 'p_hwe_unaff', 'logp_hwe_unaff', 'N_Mendel'], ['rs2283802', '22', '21784722', '0.2593', '4', '2', '0', '0.638', '0.195179', '0.638', '0.195179', '0']],s=[['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat'], ['101', '1', '0.04', '0', '2', '0', 'PROBLEM', 'nan', '-0.03355']]/n## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner
    118. 

  118. 

  119. @----------------------------------------------------------@
    120. 

  120. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    121. 

  121. |----------------------------------------------------------|
    122. 

  122. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    123. 

  123. |----------------------------------------------------------|
    124. 

  124. |  For documentation, citation & bug-report instructions:  |
    125. 

  125. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    126. 

  126. @----------------------------------------------------------@
    127. 

  127. 

  128. Skipping web check... [ --noweb ] 
    129. 

  129. Writing this text to log file [ tinywga.log ]
    130. 

  130. Analysis started: Wed May 19 15:15:38 2010
    131. 

  131. 

  132. Options in effect:
    133. 

  133. 	--noweb
    134. 

  134. 	--out tinywga
    135. 

  135. 	--bfile /opt/galaxy/test-data/tinywga
    136. 

  136. 	--mind 1.0
    137. 

  137. 	--geno 1.0
    138. 

  138. 	--maf 0.0
    139. 

  139. 	--freq
    140. 

  140. 

  141. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    142. 

  142. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    143. 

  143. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    144. 

  144. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    145. 

  145. 40 individuals with nonmissing phenotypes
    146. 

  146. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    147. 

  147. Missing phenotype value is also -9
    148. 

  148. 10 cases, 30 controls and 0 missing
    149. 

  149. 21 males, 19 females, and 0 of unspecified sex
    150. 

  150. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    151. 

  151. Detected that binary PED file is v1.00 SNP-major mode
    152. 

  152. Before frequency and genotyping pruning, there are 25 SNPs
    153. 

  153. 27 founders and 13 non-founders found
    154. 

  154. Writing allele frequencies (founders-only) to [ tinywga.frq ] 
    155. 

  155. 

  156. Analysis finished: Wed May 19 15:15:38 2010
    157. 

  157. 

  158. 

  159. @----------------------------------------------------------@
    160. 

  160. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    161. 

  161. |----------------------------------------------------------|
    162. 

  162. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    163. 

  163. |----------------------------------------------------------|
    164. 

  164. |  For documentation, citation & bug-report instructions:  |
    165. 

  165. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    166. 

  166. @----------------------------------------------------------@
    167. 

  167. 

  168. Skipping web check... [ --noweb ] 
    169. 

  169. Writing this text to log file [ tinywga.log ]
    170. 

  170. Analysis started: Wed May 19 15:15:38 2010
    171. 

  171. 

  172. Options in effect:
    173. 

  173. 	--noweb
    174. 

  174. 	--out tinywga
    175. 

  175. 	--bfile /opt/galaxy/test-data/tinywga
    176. 

  176. 	--mind 1.0
    177. 

  177. 	--geno 1.0
    178. 

  178. 	--maf 0.0
    179. 

  179. 	--hwe 0.0
    180. 

  180. 	--missing
    181. 

  181. 	--hardy
    182. 

  182. 

  183. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    184. 

  184. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    185. 

  185. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    186. 

  186. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    187. 

  187. 40 individuals with nonmissing phenotypes
    188. 

  188. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    189. 

  189. Missing phenotype value is also -9
    190. 

  190. 10 cases, 30 controls and 0 missing
    191. 

  191. 21 males, 19 females, and 0 of unspecified sex
    192. 

  192. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    193. 

  193. Detected that binary PED file is v1.00 SNP-major mode
    194. 

  194. Before frequency and genotyping pruning, there are 25 SNPs
    195. 

  195. 27 founders and 13 non-founders found
    196. 

  196. Writing Hardy-Weinberg tests (founders-only) to [ tinywga.hwe ] 
    197. 

  197. 0 markers to be excluded based on HWE test ( p <= 0 )
    198. 

  198. 	0 markers failed HWE test in cases
    199. 

  199. 	0 markers failed HWE test in controls
    200. 

  200. Writing individual missingness information to [ tinywga.imiss ] 
    201. 

  201. Writing locus missingness information to [ tinywga.lmiss ] 
    202. 

  202. Total genotyping rate in remaining individuals is 0.995
    203. 

  203. 0 SNPs failed missingness test ( GENO > 1 )
    204. 

  204. 0 SNPs failed frequency test ( MAF < 0 )
    205. 

  205. After frequency and genotyping pruning, there are 25 SNPs
    206. 

  206. After filtering, 10 cases, 30 controls and 0 missing
    207. 

  207. After filtering, 21 males, 19 females, and 0 of unspecified sex
    208. 

  208. 

  209. Analysis finished: Wed May 19 15:15:38 2010
    210. 

  210. 

  211. 

  212. @----------------------------------------------------------@
    213. 

  213. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    214. 

  214. |----------------------------------------------------------|
    215. 

  215. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    216. 

  216. |----------------------------------------------------------|
    217. 

  217. |  For documentation, citation & bug-report instructions:  |
    218. 

  218. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    219. 

  219. @----------------------------------------------------------@
    220. 

  220. 

  221. Skipping web check... [ --noweb ] 
    222. 

  222. Writing this text to log file [ tinywga.log ]
    223. 

  223. Analysis started: Wed May 19 15:15:38 2010
    224. 

  224. 

  225. Options in effect:
    226. 

  226. 	--noweb
    227. 

  227. 	--out tinywga
    228. 

  228. 	--bfile /opt/galaxy/test-data/tinywga
    229. 

  229. 	--mind 1.0
    230. 

  230. 	--geno 1.0
    231. 

  231. 	--maf 0.0
    232. 

  232. 	--mendel
    233. 

  233. 

  234. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    235. 

  235. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    236. 

  236. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    237. 

  237. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    238. 

  238. 40 individuals with nonmissing phenotypes
    239. 

  239. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    240. 

  240. Missing phenotype value is also -9
    241. 

  241. 10 cases, 30 controls and 0 missing
    242. 

  242. 21 males, 19 females, and 0 of unspecified sex
    243. 

  243. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    244. 

  244. Detected that binary PED file is v1.00 SNP-major mode
    245. 

  245. Before frequency and genotyping pruning, there are 25 SNPs
    246. 

  246. 27 founders and 13 non-founders found
    247. 

  247. Total genotyping rate in remaining individuals is 0.995
    248. 

  248. 0 SNPs failed missingness test ( GENO > 1 )
    249. 

  249. 0 SNPs failed frequency test ( MAF < 0 )
    250. 

  250. After frequency and genotyping pruning, there are 25 SNPs
    251. 

  251. After filtering, 10 cases, 30 controls and 0 missing
    252. 

  252. After filtering, 21 males, 19 females, and 0 of unspecified sex
    253. 

  253. 14 nuclear families, 1 founder singletons found
    254. 

  254. 13 non-founders with 2 parents in 13 nuclear families
    255. 

  255. 0 non-founders without 2 parents in 0 nuclear families
    256. 

  256. 10 affected offspring trios
    257. 

  257. 0 phenotypically discordant parent pairs found
    258. 

  258. Converting data to Individual-major format
    259. 

  259. Writing all Mendel errors to [ tinywga.mendel ]
    260. 

  260. Writing per-offspring Mendel summary to [ tinywga.imendel ]
    261. 

  261. Writing per-family Mendel summary to [ tinywga.fmendel ]
    262. 

  262. Writing per-locus Mendel summary to [ tinywga.lmendel ]
    263. 

  263. 0 Mendel errors detected in total
    264. 

  264. 

  265. Analysis finished: Wed May 19 15:15:38 2010
    266. 

  266. 

  267. 

  268. @----------------------------------------------------------@
    269. 

  269. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    270. 

  270. |----------------------------------------------------------|
    271. 

  271. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    272. 

  272. |----------------------------------------------------------|
    273. 

  273. |  For documentation, citation & bug-report instructions:  |
    274. 

  274. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    275. 

  275. @----------------------------------------------------------@
    276. 

  276. 

  277. Skipping web check... [ --noweb ] 
    278. 

  278. Writing this text to log file [ tinywga.log ]
    279. 

  279. Analysis started: Wed May 19 15:15:38 2010
    280. 

  280. 

  281. Options in effect:
    282. 

  282. 	--noweb
    283. 

  283. 	--out tinywga
    284. 

  284. 	--bfile /opt/galaxy/test-data/tinywga
    285. 

  285. 	--mind 1.0
    286. 

  286. 	--geno 1.0
    287. 

  287. 	--maf 0.0
    288. 

  288. 	--check-sex
    289. 

  289. 

  290. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    291. 

  291. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    292. 

  292. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    293. 

  293. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    294. 

  294. 40 individuals with nonmissing phenotypes
    295. 

  295. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    296. 

  296. Missing phenotype value is also -9
    297. 

  297. 10 cases, 30 controls and 0 missing
    298. 

  298. 21 males, 19 females, and 0 of unspecified sex
    299. 

  299. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    300. 

  300. Detected that binary PED file is v1.00 SNP-major mode
    301. 

  301. Before frequency and genotyping pruning, there are 25 SNPs
    302. 

  302. 27 founders and 13 non-founders found
    303. 

  303. Total genotyping rate in remaining individuals is 0.995
    304. 

  304. 0 SNPs failed missingness test ( GENO > 1 )
    305. 

  305. 0 SNPs failed frequency test ( MAF < 0 )
    306. 

  306. After frequency and genotyping pruning, there are 25 SNPs
    307. 

  307. After filtering, 10 cases, 30 controls and 0 missing
    308. 

  308. After filtering, 21 males, 19 females, and 0 of unspecified sex
    309. 

  309. Converting data to Individual-major format
    310. 

  310. Writing X-chromosome sex check results to [ tinywga.sexcheck ] 
    311. 

  311. 

  312. Analysis finished: Wed May 19 15:15:38 2010
    313. 

  313. 

  314. ## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner
    315. 

  315. 

  316. 

  317. 

  318. @----------------------------------------------------------@
    319. 

  319. 

  320. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    321. 

  321. 

  322. |----------------------------------------------------------|
    323. 

  323. 

  324. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    325. 

  325. 

  326. |----------------------------------------------------------|
    327. 

  327. 

  328. |  For documentation, citation & bug-report instructions:  |
    329. 

  329. 

  330. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    331. 

  331. 

  332. @----------------------------------------------------------@
    333. 

  333. 

  334. 

  335. 

  336. Skipping web check... [ --noweb ] 
    337. 

  337. 

  338. Writing this text to log file [ tinywga.log ]
    339. 

  339. 

  340. Analysis started: Wed May 19 15:15:38 2010
    341. 

  341. 

  342. 

  343. 

  344. Options in effect:
    345. 

  345. 

  346. 	--noweb
    347. 

  347. 

  348. 	--bfile /opt/galaxy/test-data/tinywga
    349. 

  349. 

  350. 	--indep-pairwise 40 20 0.5
    351. 

  351. 

  352. 	--out tinywga
    353. 

  353. 

  354. 

  355. 

  356. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    357. 

  357. 

  358. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    359. 

  359. 

  360. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    361. 

  361. 

  362. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    363. 

  363. 

  364. 40 individuals with nonmissing phenotypes
    365. 

  365. 

  366. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    367. 

  367. 

  368. Missing phenotype value is also -9
    369. 

  369. 

  370. 10 cases, 30 controls and 0 missing
    371. 

  371. 

  372. 21 males, 19 females, and 0 of unspecified sex
    373. 

  373. 

  374. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    375. 

  375. 

  376. Detected that binary PED file is v1.00 SNP-major mode
    377. 

  377. 

  378. Before frequency and genotyping pruning, there are 25 SNPs
    379. 

  379. 

  380. 27 founders and 13 non-founders found
    381. 

  381. 

  382. Total genotyping rate in remaining individuals is 0.995
    383. 

  383. 

  384. 0 SNPs failed missingness test ( GENO > 1 )
    385. 

  385. 

  386. 0 SNPs failed frequency test ( MAF < 0 )
    387. 

  387. 

  388. After frequency and genotyping pruning, there are 25 SNPs
    389. 

  389. 

  390. After filtering, 10 cases, 30 controls and 0 missing
    391. 

  391. 

  392. After filtering, 21 males, 19 females, and 0 of unspecified sex
    393. 

  393. 

  394. Performing LD-based pruning...
    395. 

  395. 

  396. Writing pruned-in SNPs to [ tinywga.prune.in ]
    397. 

  397. 

  398. Writing pruned-out SNPs to [ tinywga.prune.out ]
    399. 

  399. 

  400. Scanning from chromosome 22 to 22
    401. 

  401. 

  402. 

  403. 

  404. Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]
    405. 

  405. 

  406. For chromosome 22, 11 SNPs pruned out, 14 remaining
    407. 

  407. 

  408. 

  409. 

  410. Analysis finished: Wed May 19 15:15:38 2010
    411. 

  411. 

  412. 

  413. 

  414. 

  415. 

  416. 

  417. 

  418. @----------------------------------------------------------@
    419. 

  419. 

  420. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    421. 

  421. 

  422. |----------------------------------------------------------|
    423. 

  423. 

  424. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    425. 

  425. 

  426. |----------------------------------------------------------|
    427. 

  427. 

  428. |  For documentation, citation & bug-report instructions:  |
    429. 

  429. 

  430. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    431. 

  431. 

  432. @----------------------------------------------------------@
    433. 

  433. 

  434. 

  435. 

  436. Skipping web check... [ --noweb ] 
    437. 

  437. 

  438. Writing this text to log file [ ldp_tinywga.log ]
    439. 

  439. 

  440. Analysis started: Wed May 19 15:15:38 2010
    441. 

  441. 

  442. 

  443. 

  444. Options in effect:
    445. 

  445. 

  446. 	--noweb
    447. 

  447. 

  448. 	--bfile /opt/galaxy/test-data/tinywga
    449. 

  449. 

  450. 	--extract tinywga.prune.in
    451. 

  451. 

  452. 	--make-bed
    453. 

  453. 

  454. 	--out ldp_tinywga
    455. 

  455. 

  456. 

  457. 

  458. Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
    459. 

  459. 

  460. 25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
    461. 

  461. 

  462. Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
    463. 

  463. 

  464. 40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
    465. 

  465. 

  466. 40 individuals with nonmissing phenotypes
    467. 

  467. 

  468. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    469. 

  469. 

  470. Missing phenotype value is also -9
    471. 

  471. 

  472. 10 cases, 30 controls and 0 missing
    473. 

  473. 

  474. 21 males, 19 females, and 0 of unspecified sex
    475. 

  475. 

  476. Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
    477. 

  477. 

  478. Detected that binary PED file is v1.00 SNP-major mode
    479. 

  479. 

  480. Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read
    481. 

  481. 

  482. Before frequency and genotyping pruning, there are 14 SNPs
    483. 

  483. 

  484. 27 founders and 13 non-founders found
    485. 

  485. 

  486. Total genotyping rate in remaining individuals is 0.991071
    487. 

  487. 

  488. 0 SNPs failed missingness test ( GENO > 1 )
    489. 

  489. 

  490. 0 SNPs failed frequency test ( MAF < 0 )
    491. 

  491. 

  492. After frequency and genotyping pruning, there are 14 SNPs
    493. 

  493. 

  494. After filtering, 10 cases, 30 controls and 0 missing
    495. 

  495. 

  496. After filtering, 21 males, 19 females, and 0 of unspecified sex
    497. 

  497. 

  498. Writing pedigree information to [ ldp_tinywga.fam ] 
    499. 

  499. 

  500. Writing map (extended format) information to [ ldp_tinywga.bim ] 
    501. 

  501. 

  502. Writing genotype bitfile to [ ldp_tinywga.bed ] 
    503. 

  503. 

  504. Using (default) SNP-major mode
    505. 

  505. 

  506. 

  507. 

  508. Analysis finished: Wed May 19 15:15:38 2010
    509. 

  509. 

  510. 

  511. 

  512. 

  513. 

  514. 

  515. 

  516. @----------------------------------------------------------@
    517. 

  517. 

  518. |        PLINK!       |     v1.06      |   24/Apr/2009     |
    519. 

  519. 

  520. |----------------------------------------------------------|
    521. 

  521. 

  522. |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
    523. 

  523. 

  524. |----------------------------------------------------------|
    525. 

  525. 

  526. |  For documentation, citation & bug-report instructions:  |
    527. 

  527. 

  528. |        http://pngu.mgh.harvard.edu/purcell/plink/        |
    529. 

  529. 

  530. @----------------------------------------------------------@
    531. 

  531. 

  532. 

  533. 

  534. Skipping web check... [ --noweb ] 
    535. 

  535. 

  536. Writing this text to log file [ tinywga.log ]
    537. 

  537. 

  538. Analysis started: Wed May 19 15:15:38 2010
    539. 

  539. 

  540. 

  541. 

  542. Options in effect:
    543. 

  543. 

  544. 	--noweb
    545. 

  545. 

  546. 	--bfile ldp_tinywga
    547. 

  547. 

  548. 	--het
    549. 

  549. 

  550. 	--out tinywga
    551. 

  551. 

  552. 

  553. 

  554. Reading map (extended format) from [ ldp_tinywga.bim ] 
    555. 

  555. 

  556. 14 markers to be included from [ ldp_tinywga.bim ]
    557. 

  557. 

  558. Reading pedigree information from [ ldp_tinywga.fam ] 
    559. 

  559. 

  560. 40 individuals read from [ ldp_tinywga.fam ] 
    561. 

  561. 

  562. 40 individuals with nonmissing phenotypes
    563. 

  563. 

  564. Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
    565. 

  565. 

  566. Missing phenotype value is also -9
    567. 

  567. 

  568. 10 cases, 30 controls and 0 missing
    569. 

  569. 

  570. 21 males, 19 females, and 0 of unspecified sex
    571. 

  571. 

  572. Reading genotype bitfile from [ ldp_tinywga.bed ] 
    573. 

  573. 

  574. Detected that binary PED file is v1.00 SNP-major mode
    575. 

  575. 

  576. Before frequency and genotyping pruning, there are 14 SNPs
    577. 

  577. 

  578. 27 founders and 13 non-founders found
    579. 

  579. 

  580. Total genotyping rate in remaining individuals is 0.991071
    581. 

  581. 

  582. 0 SNPs failed missingness test ( GENO > 1 )
    583. 

  583. 

  584. 0 SNPs failed frequency test ( MAF < 0 )
    585. 

  585. 

  586. After frequency and genotyping pruning, there are 14 SNPs
    587. 

  587. 

  588. After filtering, 10 cases, 30 controls and 0 missing
    589. 

  589. 

  590. After filtering, 21 males, 19 females, and 0 of unspecified sex
    591. 

  591. 

  592. 

  593. 

  594.  **Warning** this analysis typically requires whole-genome level data
    595. 

  595. 

  596.              to give accurate results 
    597. 

  597. 

  598. 

  599. 

  600. Converting data to Individual-major format
    601. 

  601. 

  602. Writing individual heterozygosity information to [ tinywga.het ] 
    603. 

  603. 

  604. 

  605. 

  606. Analysis finished: Wed May 19 15:15:38 2010
    607. 

  607. 

  608. 

  609. 

  610. 

  611. 

  612. </pre></div></body></html>
    613. 

  613. 

  614. <hr>
    615.