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

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 12<h4>
 13<div>Output from Rgenetics QC report tool run at 19/05/2010 15:15:46<br>
 14</h4>
 15</div><div><h4>(Click any preview image to download a full sized PDF version)</h4><br><ol>
 16<table cellpadding="5" border="0">
 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<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<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</a></td><td>All tinywga QC Plots joined into a single pdf</td><td>&nbsp;</td></tr>
 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</a></td><td>All tinywga QC Plots 3 by 3 to a page</td><td>&nbsp;</td></tr>
 23<tr><td><a href="tinywga_logphweunaff.pdf"><img src="tinywga_logphweunaff.jpg" alt="Marker HWE" hspace="10" align="middle">
 24</a></td><td>Marker HWE</td><td><a href="Ranked_Marker_HWE.xls">Worst data</a></td></tr>
 25<tr><td><a href="tinywga_logphweunaff_cum.pdf"><img src="tinywga_logphweunaff_cum.jpg" alt="Ranked Marker HWE" hspace="10" align="middle">
 26</a></td><td>Ranked Marker HWE</td><td>&nbsp;</td></tr>
 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</a></td><td>LogQQ plot Marker HWE</td><td>&nbsp;</td></tr>
 29<tr><td><a href="tinywga_missfrac.pdf"><img src="tinywga_missfrac.jpg" alt="Marker Missing Genotype" hspace="10" align="middle">
 30</a></td><td>Marker Missing Genotype</td><td><a href="Ranked_Marker_Missing_Genotype.xls">Worst data</a></td></tr>
 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</a></td><td>Ranked Marker Missing Genotype</td><td>&nbsp;</td></tr>
 33<tr><td><a href="tinywga_maf.pdf"><img src="tinywga_maf.jpg" alt="Marker MAF" hspace="10" align="middle">
 34</a></td><td>Marker MAF</td><td><a href="Ranked_Marker_MAF.xls">Worst data</a></td></tr>
 35<tr><td><a href="tinywga_maf_cum.pdf"><img src="tinywga_maf_cum.jpg" alt="Ranked Marker MAF" hspace="10" align="middle">
 36</a></td><td>Ranked Marker MAF</td><td>&nbsp;</td></tr>
 37<tr><td><a href="tinywga_fracmiss.pdf"><img src="tinywga_fracmiss.jpg" alt="Subject Missing Genotype" hspace="10" align="middle">
 38</a></td><td>Subject Missing Genotype</td><td><a href="Ranked_Subject_Missing_Genotype.xls">Worst data</a></td></tr>
 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</a></td><td>Ranked Subject Missing Genotype</td><td>&nbsp;</td></tr>
 41<tr><td><a href="tinywga_s_het.pdf"><img src="tinywga_s_het.jpg" alt="Subject F Statistic" hspace="10" align="middle">
 42</a></td><td>Subject F Statistic</td><td>&nbsp;</td></tr>
 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</a></td><td>Ranked Subject F Statistic</td><td>&nbsp;</td></tr>
 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</a></td><td>F Statistic Subject F Statistic</td><td>&nbsp;</td></tr>
 47</table><hr><h3>All output files from the QC run are available below</h3>
 48<table cellpadding="5" border="0">
 49
 50<tr><td><a href="FQNormtinywga_s_het_cum.jpg">FQNormtinywga_s_het_cum.jpg</a> (30.2 KB)</td></tr>
 51<tr><td><a href="FQNormtinywga_s_het_cum.pdf">FQNormtinywga_s_het_cum.pdf</a> (7.1 KB)</td></tr>
 52<tr><td><a href="MarkerDetails_rgQCtest1.xls">MarkerDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr>
 53<tr><td><a href="QQtinywga_logphweunaff_cum.jpg">QQtinywga_logphweunaff_cum.jpg</a> (33.0 KB)</td></tr>
 54<tr><td><a href="QQtinywga_logphweunaff_cum.pdf">QQtinywga_logphweunaff_cum.pdf</a> (6.6 KB)</td></tr>
 55<tr><td><a href="Ranked_Marker_HWE.xls">Ranked_Marker_HWE.xls</a> (763 B)</td></tr>
 56<tr><td><a href="Ranked_Marker_MAF.xls">Ranked_Marker_MAF.xls</a> (564 B)</td></tr>
 57<tr><td><a href="Ranked_Marker_Missing_Genotype.xls">Ranked_Marker_Missing_Genotype.xls</a> (659 B)</td></tr>
 58<tr><td><a href="Ranked_Subject_Missing_Genotype.xls">Ranked_Subject_Missing_Genotype.xls</a> (804 B)</td></tr>
 59<tr><td><a href="SubjectDetails_rgQCtest1.xls">SubjectDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr>
 60<tr><td><a href="ldp_tinywga.bed">ldp_tinywga.bed</a> (143 B)</td></tr>
 61<tr><td><a href="ldp_tinywga.bim">ldp_tinywga.bim</a> (392 B)</td></tr>
 62<tr><td><a href="ldp_tinywga.fam">ldp_tinywga.fam</a> (603 B)</td></tr>
 63<tr><td><a href="ldp_tinywga.log">ldp_tinywga.log</a> (2.0 KB)</td></tr>
 64<tr><td><a href="tinywga.fmendel">tinywga.fmendel</a> (378 B)</td></tr>
 65<tr><td><a href="tinywga.frq">tinywga.frq</a> (1.2 KB)</td></tr>
 66<tr><td><a href="tinywga.het">tinywga.het</a> (2.5 KB)</td></tr>
 67<tr><td><a href="tinywga.hwe">tinywga.hwe</a> (6.5 KB)</td></tr>
 68<tr><td><a href="tinywga.imendel">tinywga.imendel</a> (612 B)</td></tr>
 69<tr><td><a href="tinywga.imiss">tinywga.imiss</a> (1.9 KB)</td></tr>
 70<tr><td><a href="tinywga.lmendel">tinywga.lmendel</a> (571 B)</td></tr>
 71<tr><td><a href="tinywga.lmiss">tinywga.lmiss</a> (1.1 KB)</td></tr>
 72<tr><td><a href="tinywga.log">tinywga.log</a> (1.9 KB)</td></tr>
 73<tr><td><a href="tinywga.mendel">tinywga.mendel</a> (56 B)</td></tr>
 74<tr><td><a href="tinywga.prune.in">tinywga.prune.in</a> (140 B)</td></tr>
 75<tr><td><a href="tinywga.prune.out">tinywga.prune.out</a> (110 B)</td></tr>
 76<tr><td><a href="tinywga.sexcheck">tinywga.sexcheck</a> (2.5 KB)</td></tr>
 77<tr><td><a href="tinywga_All_3x3-0.jpg">tinywga_All_3x3-0.jpg</a> (45.2 KB)</td></tr>
 78<tr><td><a href="tinywga_All_3x3-1.jpg">tinywga_All_3x3-1.jpg</a> (19.3 KB)</td></tr>
 79<tr><td><a href="tinywga_All_3x3.pdf">tinywga_All_3x3.pdf</a> (82.4 KB)</td></tr>
 80<tr><td><a href="tinywga_All_Paged-0.jpg">tinywga_All_Paged-0.jpg</a> (13.6 KB)</td></tr>
 81<tr><td><a href="tinywga_All_Paged-1.jpg">tinywga_All_Paged-1.jpg</a> (26.3 KB)</td></tr>
 82<tr><td><a href="tinywga_All_Paged-10.jpg">tinywga_All_Paged-10.jpg</a> (31.4 KB)</td></tr>
 83<tr><td><a href="tinywga_All_Paged-11.jpg">tinywga_All_Paged-11.jpg</a> (29.8 KB)</td></tr>
 84<tr><td><a href="tinywga_All_Paged-2.jpg">tinywga_All_Paged-2.jpg</a> (32.3 KB)</td></tr>
 85<tr><td><a href="tinywga_All_Paged-3.jpg">tinywga_All_Paged-3.jpg</a> (11.1 KB)</td></tr>
 86<tr><td><a href="tinywga_All_Paged-4.jpg">tinywga_All_Paged-4.jpg</a> (26.7 KB)</td></tr>
 87<tr><td><a href="tinywga_All_Paged-5.jpg">tinywga_All_Paged-5.jpg</a> (18.4 KB)</td></tr>
 88<tr><td><a href="tinywga_All_Paged-6.jpg">tinywga_All_Paged-6.jpg</a> (28.1 KB)</td></tr>
 89<tr><td><a href="tinywga_All_Paged-7.jpg">tinywga_All_Paged-7.jpg</a> (11.9 KB)</td></tr>
 90<tr><td><a href="tinywga_All_Paged-8.jpg">tinywga_All_Paged-8.jpg</a> (29.6 KB)</td></tr>
 91<tr><td><a href="tinywga_All_Paged-9.jpg">tinywga_All_Paged-9.jpg</a> (17.9 KB)</td></tr>
 92<tr><td><a href="tinywga_All_Paged.pdf">tinywga_All_Paged.pdf</a> (81.9 KB)</td></tr>
 93<tr><td><a href="tinywga_fracmiss.jpg">tinywga_fracmiss.jpg</a> (12.0 KB)</td></tr>
 94<tr><td><a href="tinywga_fracmiss.pdf">tinywga_fracmiss.pdf</a> (6.4 KB)</td></tr>
 95<tr><td><a href="tinywga_fracmiss_cum.jpg">tinywga_fracmiss_cum.jpg</a> (30.0 KB)</td></tr>
 96<tr><td><a href="tinywga_fracmiss_cum.pdf">tinywga_fracmiss_cum.pdf</a> (7.0 KB)</td></tr>
 97<tr><td><a href="tinywga_logphweunaff.jpg">tinywga_logphweunaff.jpg</a> (13.6 KB)</td></tr>
 98<tr><td><a href="tinywga_logphweunaff.pdf">tinywga_logphweunaff.pdf</a> (5.7 KB)</td></tr>
 99<tr><td><a href="tinywga_logphweunaff_cum.jpg">tinywga_logphweunaff_cum.jpg</a> (26.8 KB)</td></tr>
100<tr><td><a href="tinywga_logphweunaff_cum.pdf">tinywga_logphweunaff_cum.pdf</a> (5.8 KB)</td></tr>
101<tr><td><a href="tinywga_maf.jpg">tinywga_maf.jpg</a> (18.5 KB)</td></tr>
102<tr><td><a href="tinywga_maf.pdf">tinywga_maf.pdf</a> (6.4 KB)</td></tr>
103<tr><td><a href="tinywga_maf_cum.jpg">tinywga_maf_cum.jpg</a> (28.5 KB)</td></tr>
104<tr><td><a href="tinywga_maf_cum.pdf">tinywga_maf_cum.pdf</a> (6.0 KB)</td></tr>
105<tr><td><a href="tinywga_missfrac.jpg">tinywga_missfrac.jpg</a> (11.1 KB)</td></tr>
106<tr><td><a href="tinywga_missfrac.pdf">tinywga_missfrac.pdf</a> (5.9 KB)</td></tr>
107<tr><td><a href="tinywga_missfrac_cum.jpg">tinywga_missfrac_cum.jpg</a> (27.3 KB)</td></tr>
108<tr><td><a href="tinywga_missfrac_cum.pdf">tinywga_missfrac_cum.pdf</a> (5.9 KB)</td></tr>
109<tr><td><a href="tinywga_s_het.jpg">tinywga_s_het.jpg</a> (18.0 KB)</td></tr>
110<tr><td><a href="tinywga_s_het.pdf">tinywga_s_het.pdf</a> (6.8 KB)</td></tr>
111<tr><td><a href="tinywga_s_het_cum.jpg">tinywga_s_het_cum.jpg</a> (31.9 KB)</td></tr>
112<tr><td><a href="tinywga_s_het_cum.pdf">tinywga_s_het_cum.pdf</a> (7.3 KB)</td></tr>
113</table><h4>QC run log contents</h4><pre>## subject reports starting at 19/05/2010 15:15:38
114## imissfile /opt/galaxy/test-data/rgtestouts/rgQC/tinywga.imiss contained 40 ids
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
116hwe header testpos=2,ppos=8,snppos=1
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
119@----------------------------------------------------------@
120|        PLINK!       |     v1.06      |   24/Apr/2009     |
121|----------------------------------------------------------|
122|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
123|----------------------------------------------------------|
124|  For documentation, citation & bug-report instructions:  |
125|        http://pngu.mgh.harvard.edu/purcell/plink/        |
126@----------------------------------------------------------@
127
128Skipping web check... [ --noweb ] 
129Writing this text to log file [ tinywga.log ]
130Analysis started: Wed May 19 15:15:38 2010
131
132Options in effect:
133	--noweb
134	--out tinywga
135	--bfile /opt/galaxy/test-data/tinywga
136	--mind 1.0
137	--geno 1.0
138	--maf 0.0
139	--freq
140
141Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
14225 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
143Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
14440 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
14540 individuals with nonmissing phenotypes
146Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
147Missing phenotype value is also -9
14810 cases, 30 controls and 0 missing
14921 males, 19 females, and 0 of unspecified sex
150Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
151Detected that binary PED file is v1.00 SNP-major mode
152Before frequency and genotyping pruning, there are 25 SNPs
15327 founders and 13 non-founders found
154Writing allele frequencies (founders-only) to [ tinywga.frq ] 
155
156Analysis finished: Wed May 19 15:15:38 2010
157
158
159@----------------------------------------------------------@
160|        PLINK!       |     v1.06      |   24/Apr/2009     |
161|----------------------------------------------------------|
162|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
163|----------------------------------------------------------|
164|  For documentation, citation & bug-report instructions:  |
165|        http://pngu.mgh.harvard.edu/purcell/plink/        |
166@----------------------------------------------------------@
167
168Skipping web check... [ --noweb ] 
169Writing this text to log file [ tinywga.log ]
170Analysis started: Wed May 19 15:15:38 2010
171
172Options in effect:
173	--noweb
174	--out tinywga
175	--bfile /opt/galaxy/test-data/tinywga
176	--mind 1.0
177	--geno 1.0
178	--maf 0.0
179	--hwe 0.0
180	--missing
181	--hardy
182
183Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
18425 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
185Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
18640 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
18740 individuals with nonmissing phenotypes
188Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
189Missing phenotype value is also -9
19010 cases, 30 controls and 0 missing
19121 males, 19 females, and 0 of unspecified sex
192Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
193Detected that binary PED file is v1.00 SNP-major mode
194Before frequency and genotyping pruning, there are 25 SNPs
19527 founders and 13 non-founders found
196Writing Hardy-Weinberg tests (founders-only) to [ tinywga.hwe ] 
1970 markers to be excluded based on HWE test ( p <= 0 )
198	0 markers failed HWE test in cases
199	0 markers failed HWE test in controls
200Writing individual missingness information to [ tinywga.imiss ] 
201Writing locus missingness information to [ tinywga.lmiss ] 
202Total genotyping rate in remaining individuals is 0.995
2030 SNPs failed missingness test ( GENO > 1 )
2040 SNPs failed frequency test ( MAF < 0 )
205After frequency and genotyping pruning, there are 25 SNPs
206After filtering, 10 cases, 30 controls and 0 missing
207After filtering, 21 males, 19 females, and 0 of unspecified sex
208
209Analysis finished: Wed May 19 15:15:38 2010
210
211
212@----------------------------------------------------------@
213|        PLINK!       |     v1.06      |   24/Apr/2009     |
214|----------------------------------------------------------|
215|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
216|----------------------------------------------------------|
217|  For documentation, citation & bug-report instructions:  |
218|        http://pngu.mgh.harvard.edu/purcell/plink/        |
219@----------------------------------------------------------@
220
221Skipping web check... [ --noweb ] 
222Writing this text to log file [ tinywga.log ]
223Analysis started: Wed May 19 15:15:38 2010
224
225Options in effect:
226	--noweb
227	--out tinywga
228	--bfile /opt/galaxy/test-data/tinywga
229	--mind 1.0
230	--geno 1.0
231	--maf 0.0
232	--mendel
233
234Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
23525 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
236Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
23740 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
23840 individuals with nonmissing phenotypes
239Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
240Missing phenotype value is also -9
24110 cases, 30 controls and 0 missing
24221 males, 19 females, and 0 of unspecified sex
243Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
244Detected that binary PED file is v1.00 SNP-major mode
245Before frequency and genotyping pruning, there are 25 SNPs
24627 founders and 13 non-founders found
247Total genotyping rate in remaining individuals is 0.995
2480 SNPs failed missingness test ( GENO > 1 )
2490 SNPs failed frequency test ( MAF < 0 )
250After frequency and genotyping pruning, there are 25 SNPs
251After filtering, 10 cases, 30 controls and 0 missing
252After filtering, 21 males, 19 females, and 0 of unspecified sex
25314 nuclear families, 1 founder singletons found
25413 non-founders with 2 parents in 13 nuclear families
2550 non-founders without 2 parents in 0 nuclear families
25610 affected offspring trios
2570 phenotypically discordant parent pairs found
258Converting data to Individual-major format
259Writing all Mendel errors to [ tinywga.mendel ]
260Writing per-offspring Mendel summary to [ tinywga.imendel ]
261Writing per-family Mendel summary to [ tinywga.fmendel ]
262Writing per-locus Mendel summary to [ tinywga.lmendel ]
2630 Mendel errors detected in total
264
265Analysis finished: Wed May 19 15:15:38 2010
266
267
268@----------------------------------------------------------@
269|        PLINK!       |     v1.06      |   24/Apr/2009     |
270|----------------------------------------------------------|
271|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
272|----------------------------------------------------------|
273|  For documentation, citation & bug-report instructions:  |
274|        http://pngu.mgh.harvard.edu/purcell/plink/        |
275@----------------------------------------------------------@
276
277Skipping web check... [ --noweb ] 
278Writing this text to log file [ tinywga.log ]
279Analysis started: Wed May 19 15:15:38 2010
280
281Options in effect:
282	--noweb
283	--out tinywga
284	--bfile /opt/galaxy/test-data/tinywga
285	--mind 1.0
286	--geno 1.0
287	--maf 0.0
288	--check-sex
289
290Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
29125 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
292Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
29340 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
29440 individuals with nonmissing phenotypes
295Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
296Missing phenotype value is also -9
29710 cases, 30 controls and 0 missing
29821 males, 19 females, and 0 of unspecified sex
299Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
300Detected that binary PED file is v1.00 SNP-major mode
301Before frequency and genotyping pruning, there are 25 SNPs
30227 founders and 13 non-founders found
303Total genotyping rate in remaining individuals is 0.995
3040 SNPs failed missingness test ( GENO > 1 )
3050 SNPs failed frequency test ( MAF < 0 )
306After frequency and genotyping pruning, there are 25 SNPs
307After filtering, 10 cases, 30 controls and 0 missing
308After filtering, 21 males, 19 females, and 0 of unspecified sex
309Converting data to Individual-major format
310Writing X-chromosome sex check results to [ tinywga.sexcheck ] 
311
312Analysis finished: Wed May 19 15:15:38 2010
313
314## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner
315
316
317
318@----------------------------------------------------------@
319
320|        PLINK!       |     v1.06      |   24/Apr/2009     |
321
322|----------------------------------------------------------|
323
324|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
325
326|----------------------------------------------------------|
327
328|  For documentation, citation & bug-report instructions:  |
329
330|        http://pngu.mgh.harvard.edu/purcell/plink/        |
331
332@----------------------------------------------------------@
333
334
335
336Skipping web check... [ --noweb ] 
337
338Writing this text to log file [ tinywga.log ]
339
340Analysis started: Wed May 19 15:15:38 2010
341
342
343
344Options in effect:
345
346	--noweb
347
348	--bfile /opt/galaxy/test-data/tinywga
349
350	--indep-pairwise 40 20 0.5
351
352	--out tinywga
353
354
355
356Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
357
35825 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
359
360Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
361
36240 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
363
36440 individuals with nonmissing phenotypes
365
366Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
367
368Missing phenotype value is also -9
369
37010 cases, 30 controls and 0 missing
371
37221 males, 19 females, and 0 of unspecified sex
373
374Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
375
376Detected that binary PED file is v1.00 SNP-major mode
377
378Before frequency and genotyping pruning, there are 25 SNPs
379
38027 founders and 13 non-founders found
381
382Total genotyping rate in remaining individuals is 0.995
383
3840 SNPs failed missingness test ( GENO > 1 )
385
3860 SNPs failed frequency test ( MAF < 0 )
387
388After frequency and genotyping pruning, there are 25 SNPs
389
390After filtering, 10 cases, 30 controls and 0 missing
391
392After filtering, 21 males, 19 females, and 0 of unspecified sex
393
394Performing LD-based pruning...
395
396Writing pruned-in SNPs to [ tinywga.prune.in ]
397
398Writing pruned-out SNPs to [ tinywga.prune.out ]
399
400Scanning from chromosome 22 to 22
401
402
403
404Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ]
405
406For chromosome 22, 11 SNPs pruned out, 14 remaining
407
408
409
410Analysis finished: Wed May 19 15:15:38 2010
411
412
413
414
415
416
417
418@----------------------------------------------------------@
419
420|        PLINK!       |     v1.06      |   24/Apr/2009     |
421
422|----------------------------------------------------------|
423
424|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
425
426|----------------------------------------------------------|
427
428|  For documentation, citation & bug-report instructions:  |
429
430|        http://pngu.mgh.harvard.edu/purcell/plink/        |
431
432@----------------------------------------------------------@
433
434
435
436Skipping web check... [ --noweb ] 
437
438Writing this text to log file [ ldp_tinywga.log ]
439
440Analysis started: Wed May 19 15:15:38 2010
441
442
443
444Options in effect:
445
446	--noweb
447
448	--bfile /opt/galaxy/test-data/tinywga
449
450	--extract tinywga.prune.in
451
452	--make-bed
453
454	--out ldp_tinywga
455
456
457
458Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] 
459
46025 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ]
461
462Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] 
463
46440 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] 
465
46640 individuals with nonmissing phenotypes
467
468Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
469
470Missing phenotype value is also -9
471
47210 cases, 30 controls and 0 missing
473
47421 males, 19 females, and 0 of unspecified sex
475
476Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] 
477
478Detected that binary PED file is v1.00 SNP-major mode
479
480Reading list of SNPs to extract [ tinywga.prune.in ] ... 14 read
481
482Before frequency and genotyping pruning, there are 14 SNPs
483
48427 founders and 13 non-founders found
485
486Total genotyping rate in remaining individuals is 0.991071
487
4880 SNPs failed missingness test ( GENO > 1 )
489
4900 SNPs failed frequency test ( MAF < 0 )
491
492After frequency and genotyping pruning, there are 14 SNPs
493
494After filtering, 10 cases, 30 controls and 0 missing
495
496After filtering, 21 males, 19 females, and 0 of unspecified sex
497
498Writing pedigree information to [ ldp_tinywga.fam ] 
499
500Writing map (extended format) information to [ ldp_tinywga.bim ] 
501
502Writing genotype bitfile to [ ldp_tinywga.bed ] 
503
504Using (default) SNP-major mode
505
506
507
508Analysis finished: Wed May 19 15:15:38 2010
509
510
511
512
513
514
515
516@----------------------------------------------------------@
517
518|        PLINK!       |     v1.06      |   24/Apr/2009     |
519
520|----------------------------------------------------------|
521
522|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
523
524|----------------------------------------------------------|
525
526|  For documentation, citation & bug-report instructions:  |
527
528|        http://pngu.mgh.harvard.edu/purcell/plink/        |
529
530@----------------------------------------------------------@
531
532
533
534Skipping web check... [ --noweb ] 
535
536Writing this text to log file [ tinywga.log ]
537
538Analysis started: Wed May 19 15:15:38 2010
539
540
541
542Options in effect:
543
544	--noweb
545
546	--bfile ldp_tinywga
547
548	--het
549
550	--out tinywga
551
552
553
554Reading map (extended format) from [ ldp_tinywga.bim ] 
555
55614 markers to be included from [ ldp_tinywga.bim ]
557
558Reading pedigree information from [ ldp_tinywga.fam ] 
559
56040 individuals read from [ ldp_tinywga.fam ] 
561
56240 individuals with nonmissing phenotypes
563
564Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
565
566Missing phenotype value is also -9
567
56810 cases, 30 controls and 0 missing
569
57021 males, 19 females, and 0 of unspecified sex
571
572Reading genotype bitfile from [ ldp_tinywga.bed ] 
573
574Detected that binary PED file is v1.00 SNP-major mode
575
576Before frequency and genotyping pruning, there are 14 SNPs
577
57827 founders and 13 non-founders found
579
580Total genotyping rate in remaining individuals is 0.991071
581
5820 SNPs failed missingness test ( GENO > 1 )
583
5840 SNPs failed frequency test ( MAF < 0 )
585
586After frequency and genotyping pruning, there are 14 SNPs
587
588After filtering, 10 cases, 30 controls and 0 missing
589
590After filtering, 21 males, 19 females, and 0 of unspecified sex
591
592
593
594 **Warning** this analysis typically requires whole-genome level data
595
596             to give accurate results 
597
598
599
600Converting data to Individual-major format
601
602Writing individual heterozygosity information to [ tinywga.het ] 
603
604
605
606Analysis finished: Wed May 19 15:15:38 2010
607
608
609
610
611
612</pre></div></body></html>
613
614<hr>