-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathindex_plink.php
602 lines (528 loc) · 21.4 KB
/
index_plink.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
<html>
<body>
<head>
<link rel="stylesheet" href="plink.css" type="text/css">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
<title>inbix: In silico Bioinformatics Toolkit - PLINK Capabilities</title>
</head>
<font size="6" color="darkgreen"><b>inbix...</b></font>
<div style="position:absolute;right:10px;top:10px;font-size:
75%"><em>Last original <tt>inbix</tt> release is <b>v0.99p</b>
(26-Jun-2018)</div>
<h1>inbix: <em>In silico</em> Bioinformatics Toolkit - PLINK Capabilities</h1>
<font size="1" color="darkgreen">
<em>
<a href="index.php">Return to inbix</a> |
<a href="index_plink.php">Introduction to PLINK</a> |
<a href="contact.shtml">Basics</a> |
<!--
<a href="download.shtml">Download</a> |
-->
<a href="reference.shtml">Reference</a> |
<a href="data.shtml">Formats</a> |
<a href="dataman.shtml">Data management</a> |
<a href="summary.shtml">Summary stats</a> |
<a href="thresh.shtml">Filters</a> |
<a href="strat.shtml">Stratification</a> |
<a href="ibdibs.shtml">IBS/IBD</a> |
<a href="anal.shtml">Association</a> |
<a href="fanal.shtml">Family-based</a> |
<a href="perm.shtml">Permutation</a> |
<a href="ld.shtml">LD calcualtions</a> |
<a href="haplo.shtml">Haplotypes</a> |
<a href="whap.shtml">Conditional tests</a> |
<a href="proxy.shtml">Proxy association</a> |
<a href="pimputation.shtml">Imputation</a> |
<a href="dosage.shtml">Dosage data</a> |
<a href="metaanal.shtml">Meta-analysis</a> |
<a href="annot.shtml">Result annotation</a> |
<a href="clump.shtml">Clumping</a> |
<a href="grep.shtml">Gene Report</a> |
<a href="epi.shtml">Epistasis</a> |
<a href="cnv.shtml">Rare CNVs</a> |
<a href="gvar.shtml">Common CNPs</a> |
<a href="rfunc.shtml">R-plugins</a> |
<a href="psnp.shtml">SNP annotation</a> |
<a href="simulate.shtml">Simulation</a> |
<a href="profile.shtml">Profiles</a> |
<a href="ids.shtml">ID helper</a> |
<a href="res.shtml">Resources</a> |
<a href="flow.shtml">Flow chart</a> |
<a href="misc.shtml">Misc.</a> |
<a href="faq.shtml">FAQ</a>
<!--
<a href="gplink.shtml">gPLINK</a>
-->
</em></font>
</p>
<table border=0>
<tr>
<td bgcolor="lightblue" valign="top" width=20%>
<font size="1">
<a href="index.php">0. Return to the inbix home page</a> </p>
<a href="index_plink.shtml">1. Introduction to PLINK</a> </p>
<a href="contact.shtml">2. Basic information</a> </p>
<ul>
<li> <a href="contact.shtml#cite">Citing PLINK</a>
<li> <a href="contact.shtml#probs">Reporting problems</a>
<li> <a href="news.shtml">What's new?</a>
<li> <a href="pdf.shtml">PDF documentation</a>
</ul>
<a href="download.shtml">3. General notes</a> </p>
<ul>
<!--
<li> <a href="download.shtml#download">Stable download</a>
<li> <a href="download.shtml#latest">Development code</a>
-->
<li> <a href="download.shtml#general">General notes</a>
<li> <a href="download.shtml#msdos">MS-DOS notes</a>
<li> <a href="download.shtml#nix">Unix/Linux notes</a>
<li> <a href="download.shtml#compilation">Compilation</a>
<li> <a href="download.shtml#input">Using the command line</a>
<li> <a href="download.shtml#output">Viewing output files</a>
<li> <a href="changelog.shtml">Version history</a>
</ul>
<a href="reference.shtml">4. Command reference table</a> </p>
<ul>
<li> <a href="reference.shtml#options">List of options</a>
<li> <a href="reference.shtml#output">List of output files</a>
<li> <a href="newfeat.shtml">Under development</a>
</ul>
<a href="data.shtml">5. Basic usage/data formats</a>
<ul>
<li> <a href="data.shtml#plink">Running PLINK</a>
<li> <a href="data.shtml#ped">PED files</a>
<li> <a href="data.shtml#map">MAP files</a>
<li> <a href="data.shtml#tr">Transposed filesets</a>
<li> <a href="data.shtml#long">Long-format filesets</a>
<li> <a href="data.shtml#bed">Binary PED files</a>
<li> <a href="data.shtml#pheno">Alternate phenotypes</a>
<li> <a href="data.shtml#covar">Covariate files</a>
<li> <a href="data.shtml#clst">Cluster files</a>
<li> <a href="data.shtml#sets">Set files</a>
</ul>
<a href="dataman.shtml">6. Data management</a> </p>
<ul>
<li> <a href="dataman.shtml#recode">Recode</a>
<li> <a href="dataman.shtml#recode">Reorder</a>
<li> <a href="dataman.shtml#snplist">Write SNP list</a>
<li> <a href="dataman.shtml#updatemap">Update SNP map</a>
<li> <a href="dataman.shtml#updateallele">Update allele information</a>
<li> <a href="dataman.shtml#refallele">Force reference allele</a>
<li> <a href="dataman.shtml#updatefam">Update individuals</a>
<li> <a href="dataman.shtml#wrtcov">Write covariate files</a>
<li> <a href="dataman.shtml#wrtclst">Write cluster files</a>
<li> <a href="dataman.shtml#flip">Flip strand</a>
<li> <a href="dataman.shtml#flipscan">Scan for strand problem</a>
<li> <a href="dataman.shtml#merge">Merge two files</a>
<li> <a href="dataman.shtml#mergelist">Merge multiple files</a>
<li> <a href="dataman.shtml#extract">Extract SNPs</a>
<li> <a href="dataman.shtml#exclude">Remove SNPs</a>
<li> <a href="dataman.shtml#zero">Zero out sets of genotypes</a>
<li> <a href="dataman.shtml#keep">Extract Individuals</a>
<li> <a href="dataman.shtml#remove">Remove Individuals</a>
<li> <a href="dataman.shtml#filter">Filter Individuals</a>
<li> <a href="dataman.shtml#attrib">Attribute filters</a>
<li> <a href="dataman.shtml#makeset">Create a set file</a>
<li> <a href="dataman.shtml#tabset">Tabulate SNPs by sets</a>
<li> <a href="dataman.shtml#snp-qual">SNP quality scores</a>
<li> <a href="dataman.shtml#geno-qual">Genotypic quality scores</a>
</ul>
<a href="summary.shtml">7. Summary stats</a>
<ul>
<li> <a href="summary.shtml#missing">Missingness</a>
<li> <a href="summary.shtml#oblig_missing">Obligatory missingness</a>
<li> <a href="summary.shtml#clustermissing">IBM clustering</a>
<li> <a href="summary.shtml#testmiss">Missingness by phenotype</a>
<li> <a href="summary.shtml#mishap">Missingness by genotype</a>
<li> <a href="summary.shtml#hardy">Hardy-Weinberg</a>
<li> <a href="summary.shtml#freq">Allele frequencies</a>
<li> <a href="summary.shtml#prune">LD-based SNP pruning</a>
<li> <a href="summary.shtml#mendel">Mendel errors</a>
<li> <a href="summary.shtml#sexcheck">Sex check</a>
<li> <a href="summary.shtml#pederr">Pedigree errors</a>
</ul>
<a href="thresh.shtml">8. Inclusion thresholds</a>
<ul>
<li> <a href="thresh.shtml#miss2">Missing/person</a>
<li> <a href="thresh.shtml#maf">Allele frequency</a>
<li> <a href="thresh.shtml#miss1">Missing/SNP</a>
<li> <a href="thresh.shtml#hwd">Hardy-Weinberg</a>
<li> <a href="thresh.shtml#mendel">Mendel errors</a>
</ul>
<a href="strat.shtml">9. Population stratification</a>
<ul>
<li> <a href="strat.shtml#cluster">IBS clustering</a>
<li> <a href="strat.shtml#permtest">Permutation test</a>
<li> <a href="strat.shtml#options">Clustering options</a>
<li> <a href="strat.shtml#matrix">IBS matrix</a>
<li> <a href="strat.shtml#mds">Multidimensional scaling</a>
<li> <a href="strat.shtml#outlier">Outlier detection</a>
</ul>
<a href="ibdibs.shtml">10. IBS/IBD estimation</a>
<ul>
<li> <a href="ibdibs.shtml#genome">Pairwise IBD</a>
<li> <a href="ibdibs.shtml#inbreeding">Inbreeding</a>
<li> <a href="ibdibs.shtml#homo">Runs of homozygosity</a>
<li> <a href="ibdibs.shtml#segments">Shared segments</a>
</ul>
<a href="anal.shtml">11. Association</a>
<ul>
<li> <a href="anal.shtml#cc">Case/control</a>
<li> <a href="anal.shtml#fisher">Fisher's exact</a>
<li> <a href="anal.shtml#model">Full model</a>
<li> <a href="anal.shtml#strat">Stratified analysis</a>
<li> <a href="anal.shtml#homog">Tests of heterogeneity</a>
<li> <a href="anal.shtml#hotel">Hotelling's T(2) test</a>
<li> <a href="anal.shtml#qt">Quantitative trait</a>
<li> <a href="anal.shtml#qtmeans">Quantitative trait means</a>
<li> <a href="anal.shtml#qtgxe">Quantitative trait GxE</a>
<li> <a href="anal.shtml#glm">Linear and logistic models</a>
<li> <a href="anal.shtml#set">Set-based tests</a>
<li> <a href="anal.shtml#adjust">Multiple-test correction</a>
</ul>
<a href="fanal.shtml">12. Family-based association</a>
<ul>
<li> <a href="fanal.shtml#tdt">TDT</a>
<li> <a href="fanal.shtml#ptdt">ParenTDT</a>
<li> <a href="fanal.shtml#poo">Parent-of-origin</a>
<li> <a href="fanal.shtml#dfam">DFAM test</a>
<li> <a href="fanal.shtml#qfam">QFAM test</a>
</ul>
<a href="perm.shtml">13. Permutation procedures</a>
<ul>
<li> <a href="perm.shtml#perm">Basic permutation</a>
<li> <a href="perm.shtml#aperm">Adaptive permutation</a>
<li> <a href="perm.shtml#mperm">max(T) permutation</a>
<li> <a href="perm.shtml#rank">Ranked permutation</a>
<li> <a href="perm.shtml#genedropmodel">Gene-dropping</a>
<li> <a href="perm.shtml#cluster">Within-cluster</a>
<li> <a href="perm.shtml#mkphe">Permuted phenotypes files</a>
</ul>
<a href="ld.shtml">14. LD calculations</a>
<ul>
<li> <a href="ld.shtml#ld1">2 SNP pairwise LD</a>
<li> <a href="ld.shtml#ld2">N SNP pairwise LD</a>
<li> <a href="ld.shtml#tags">Tagging options</a>
<li> <a href="ld.shtml#blox">Haplotype blocks</a>
</ul>
<a href="haplo.shtml">15. Multimarker tests</a>
<ul>
<li> <a href="haplo.shtml#hap1">Imputing haplotypes</a>
<li> <a href="haplo.shtml#precomputed">Precomputed lists</a>
<li> <a href="haplo.shtml#hap2">Haplotype frequencies</a>
<li> <a href="haplo.shtml#hap3">Haplotype-based association</a>
<li> <a href="haplo.shtml#hap3c">Haplotype-based GLM tests</a>
<li> <a href="haplo.shtml#hap3b">Haplotype-based TDT</a>
<li> <a href="haplo.shtml#hap4">Haplotype imputation</a>
<li> <a href="haplo.shtml#hap5">Individual phases</a>
</ul>
<a href="whap.shtml">16. Conditional haplotype tests</a>
<ul>
<li> <a href="whap.shtml#whap1">Basic usage</a>
<li> <a href="whap.shtml#whap2">Specifying type of test</a>
<li> <a href="whap.shtml#whap3">General haplogrouping</a>
<li> <a href="whap.shtml#whap4">Covariates and other SNPs</a>
</ul>
<a href="proxy.shtml">17. Proxy association</a>
<ul>
<li> <a href="proxy.shtml#proxy1">Basic usage</a>
<li> <a href="proxy.shtml#proxy2">Refining a signal</a>
<li> <a href="proxy.shtml#proxy2b">Multiple reference SNPs</a>
<li> <a href="proxy.shtml#proxy3">Haplotype-based SNP tests</a>
</ul>
<a href="pimputation.shtml">18. Imputation (beta)</a>
<ul>
<li> <a href="pimputation.shtml#impute1">Making reference set</a>
<li> <a href="pimputation.shtml#impute2">Basic association test</a>
<li> <a href="pimputation.shtml#impute3">Modifying parameters</a>
<li> <a href="pimputation.shtml#impute4">Imputing discrete calls</a>
<li> <a href="pimputation.shtml#impute5">Verbose output options</a>
</ul>
<a href="dosage.shtml">19. Dosage data</a>
<ul>
<li> <a href="dosage.shtml#format">Input file formats</a>
<li> <a href="dosage.shtml#assoc">Association analysis</a>
<li> <a href="dosage.shtml#output">Outputting dosage data</a>
</ul>
<a href="metaanal.shtml">20. Meta-analysis</a>
<ul>
<li> <a href="metaanal.shtml#basic">Basic usage</a>
<li> <a href="metaanal.shtml#opt">Misc. options</a>
</ul>
<a href="annot.shtml">21. Annotation (when compiled with web access)</a>
<ul>
<li> <a href="annot.shtml#basic">Basic usage</a>
<li> <a href="annot.shtml#opt">Misc. options</a>
</ul>
<a href="clump.shtml">22. LD-based results clumping</a>
<ul>
<li> <a href="clump.shtml#clump1">Basic usage</a>
<li> <a href="clump.shtml#clump2">Verbose reporting</a>
<li> <a href="clump.shtml#clump3">Combining multiple studies</a>
<li> <a href="clump.shtml#clump4">Best single proxy</a>
</ul>
<a href="grep.shtml">23. Gene-based report</a>
<ul>
<li> <a href="grep.shtml#grep1">Basic usage</a>
<li> <a href="grep.shtml#grep2">Other options</a>
</ul>
<a href="epi.shtml">24. Epistasis</a>
<ul>
<li> <a href="epi.shtml#snp">SNP x SNP</a>
<li> <a href="epi.shtml#case">Case-only</a>
<li> <a href="epi.shtml#gene">Gene-based</a>
</ul>
<a href="cnv.shtml">25. Rare CNVs</a>
<ul>
<li> <a href="cnv.shtml#format">File format</a>
<li> <a href="cnv.shtml#maps">MAP file construction</a>
<li> <a href="cnv.shtml#loading">Loading CNVs</a>
<li> <a href="cnv.shtml#olap_check">Check for overlap</a>
<li> <a href="cnv.shtml#type_filter">Filter on type </a>
<li> <a href="cnv.shtml#gene_filter">Filter on genes </a>
<li> <a href="cnv.shtml#freq_filter">Filter on frequency </a>
<li> <a href="cnv.shtml#burden">Burden analysis</a>
<li> <a href="cnv.shtml#burden2">Geneset enrichment</a>
<li> <a href="cnv.shtml#assoc">Mapping loci</a>
<li> <a href="cnv.shtml#reg-assoc">Regional tests</a>
<li> <a href="cnv.shtml#qt-assoc">Quantitative traits</a>
<li> <a href="cnv.shtml#write_cnvlist">Write CNV lists</a>
<li> <a href="cnv.shtml#report">Write gene lists</a>
<li> <a href="cnv.shtml#groups">Grouping CNVs </a>
</ul>
<a href="gvar.shtml">26. Common CNPs</a>
<ul>
<li> <a href="gvar.shtml#cnv2"> CNPs/generic variants</a>
<li> <a href="gvar.shtml#cnv2b"> CNP/SNP association</a>
</ul>
<a href="rfunc.shtml">27. R-plugins</a>
<ul>
<li> <a href="rfunc.shtml#rfunc1">Basic usage</a>
<li> <a href="rfunc.shtml#rfunc2">Defining the R function</a>
<li> <a href="rfunc.shtml#rfunc2b">Example of debugging</a>
<li> <a href="rfunc.shtml#rfunc3">Installing Rserve</a>
</ul>
<a href="psnp.shtml">28. Annotation web-lookup (when compiled with web access)</a>
<ul>
<li> <a href="psnp.shtml#psnp1">Basic SNP annotation</a>
<li> <a href="psnp.shtml#psnp2">Gene-based SNP lookup</a>
<li> <a href="psnp.shtml#psnp3">Annotation sources</a>
</ul>
<a href="simulate.shtml">29. Simulation tools</a>
<ul>
<li> <a href="simulate.shtml#sim1">Basic usage</a>
<li> <a href="simulate.shtml#sim2">Resampling a population</a>
<li> <a href="simulate.shtml#sim3">Quantitative traits</a>
</ul>
<a href="profile.shtml">30. Profile scoring</a>
<ul>
<li> <a href="profile.shtml#prof1">Basic usage</a>
<li> <a href="profile.shtml#prof2">SNP subsets</a>
<li> <a href="profile.shtml#dose">Dosage data</a>
<li> <a href="profile.shtml#prof3">Misc options</a>
</ul>
<a href="ids.shtml">31. ID helper</a>
<ul>
<li> <a href="ids.shtml#ex">Overview/example</a>
<li> <a href="ids.shtml#intro">Basic usage</a>
<li> <a href="ids.shtml#check">Consistency checks</a>
<li> <a href="ids.shtml#alias">Aliases</a>
<li> <a href="ids.shtml#joint">Joint IDs</a>
<li> <a href="ids.shtml#lookup">Lookups</a>
<li> <a href="ids.shtml#replace">Replace values</a>
<li> <a href="ids.shtml#match">Match files</a>
<li> <a href="ids.shtml#qmatch">Quick match files</a>
<li> <a href="ids.shtml#misc">Misc.</a>
</ul>
<a href="res.shtml">32. Resources</a>
<ul>
<li> <a href="res.shtml#hapmap">HapMap (PLINK format)</a>
<li> <a href="res.shtml#teach">Teaching materials</a>
<li> <a href="res.shtml#mmtests">Multimarker tests</a>
<li> <a href="res.shtml#sets">Gene-set lists</a>
<li> <a href="res.shtml#glist">Gene range lists</a>
<li> <a href="res.shtml#attrib">SNP attributes</a>
</ul>
<a href="flow.shtml">33. Flow-chart</a>
<ul>
<li> <a href="flow.shtml">Order of commands</a>
</ul>
<a href="misc.shtml">34. Miscellaneous</a>
<ul>
<li> <a href="misc.shtml#opt">Command options/modifiers</a>
<li> <a href="misc.shtml#output">Association output modifiers</a>
<li> <a href="misc.shtml#species">Different species</a>
<li> <a href="misc.shtml#bugs">Known issues</a>
</ul>
<a href="faq.shtml">35. FAQ & Hints</a>
<!--
</p>
<a href="gplink.shtml">36. gPLINK</a>
<ul>
<li> <a href="gplink.shtml">gPLINK mainpage</a>
<li> <a href="gplink_tutorial/index.html">Tour of gPLINK</a>
<li> <a href="gplink.shtml#overview">Overview: using gPLINK</a>
<li> <a href="gplink.shtml#locrem">Local versus remote modes</a>
<li> <a href="gplink.shtml#start">Starting a new project</a>
<li> <a href="gplink.shtml#config">Configuring gPLINK</a>
<li> <a href="gplink.shtml#plink">Initiating PLINK jobs</a>
<li> <a href="gplink.shtml#view">Viewing PLINK output</a>
<li> <a href="gplink.shtml#hv">Integration with Haploview</a>
<li> <a href="gplink.shtml#down">Downloading gPLINK</a></p>
</ul>
-->
<a href="index.php">Return to the inbix home page</a>
</p>
</font>
</td><td width=5%>
<td valign="top">
</p>
<table border=0 width=100%>
<tr><td width=70%>
<p><font color="red"><b>New (15-May-2014)</font>: PLINK 1.9 is now <a href="plink2.shtml">available</a> for beta-testing!</b></p><hr>
<tt><font color="darkgreen"><b>PLINK</b></font></tt> is a free,
open-source whole genome association analysis toolset, designed to perform
a range of basic, large-scale analyses in a computationally efficient
manner.
</p>
The focus of <tt><font color="darkgreen"><b>PLINK</b></font></tt>
is purely on <em>analysis</em> of genotype/phenotype data, so
there is no support for steps prior to this (e.g. study design
and planning, generating genotype or CNV calls from raw data).
Through integration with <a href="gplink.shtml">gPLINK</a> and
<a href="http://www.broad.mit.edu/mpg/haploview">Haploview</a>,
there is some support for the subsequent visualization, annotation
and storage of results.
</p>
<tt><font color="darkgreen"><b>PLINK</b></font></tt> was developed by
<a href="http://zzz.bwh.harvard.edu">Shaun Purcell</a> whilst at the
Center for Human Genetic Research (<a href="http://chgr.mgh.harvard.edu">CHGR</a>),
Massachusetts General Hospital (<a
href="http://www.mgh.harvard.edu">MGH</a>), and the <a
href="http://www.broad.mit.edu">Broad Institute</a> of Harvard & MIT,
with the <a href="credits.shtml">support of others</a>.
</p>
</p>
<b><em>New in 1.07</em></b>: <a href="metaanal.shtml">meta-analysis</a>, <a href="annot.shtml">result annotation</a>
and analysis of <a href="dosage.shtml">dosage data</a>.
</p>
</td><td valign="top" align="center">
<div align="left"
style="
border-top:2px solid #225522;
border-bottom:2px solid #225522;
padding:5px;
margin:5px;
background: #CCDDFF;
background: #f0f5f0;
width:150px;">
<b><em><font color="darkgreen">Quick links</font></em></b></p>
<a href="tutorial.shtml"><tt>PLINK</tt> tutorial</a> </p>
<!-- <a href="gplink.shtml"><tt>gPLINK</tt></a> </p> -->
<a href="http://amber.mgh.harvard.edu/mailman/listinfo/plink-list">Join e-mail list</p></a>
<a href="res.shtml">Resources</a></p>
<a href="faq.shtml">FAQs</a> | <a href="pdf.shtml">PDF</a></p>
<a href="contact.shtml#cite">Citing <tt>PLINK</tt></a></p>
<a href="contact.shtml#probs">Bugs, questions?</a> </p>
</div>
</td></tr></table>
<h1> Data management</h1>
<ul>
<li> Read data in a variety of formats
<li> Recode and reorder files
<li> Merge two or more files
<li> Extracts subsets (SNPs or individuals)
<li> Flip strand of SNPs
<li> Compress data in a binary file format
</ul>
<h1>Summary statistics for quality control</h1>
<ul>
<li> Allele, genotypes frequencies, HWE tests
<li> Missing genotype rates
<li> Inbreeding, IBS and IBD statistics for individuals and pairs of individuals
<li> non-Mendelian transmission in family data
<li> Sex checks based on X chromosome SNPs
<li> Tests of non-random genotyping failure
</ul>
<h1> Population stratification detection</h1>
<ul>
<li> Complete linkage hierarchical clustering
<li> Handles virtually unlimited numbers of SNPs
<li> Multidimensional scaling analysis to visualise substructure
<li> Significance test for whether two individuals belong to the same population
<li> Constrain cluster solution by phenotype, cluster size and/or external matching criteria
<li> Perform subsequent association analyses conditional on cluster solution
</ul>
<h1> Basic association testing</h1>
<ul>
<li> Case/control
<ul>
<li> Standard allelic test
<li> Fisher's exact test
<li> Cochran-Armitage trend test
<li> Mantel-Haenszel and Breslow-Day tests for stratified samples
<li> Dominant/recessive and general models
<li> Model comparison tests (e.g. general versus multiplicative)
</ul>
<li> Family-based association (TDT, sibship tests)
<li> Quantitative traits, association and interaction
<li> Association conditional on one or more SNPs
<li> Asymptotic and empirical p-values
<li> Flexible clustered permutation scheme
<li> Analysis of genotype probability data and fractional allele coounts (post-imputation)
</ul>
<h1> Multimarker predictors, haplotypic tests</h1>
<ul>
<li> Suite of flexible, conditional haplotype tests
<li> Case/control and TDT association on the probabilistic haplotype phase
<li> A set of proxy associaiton" methods to study single SNP associations in their local haplotypic context
<li> Imputation heuristic, to test untyped SNPs given a reference panel
</ul>
<h1> Copy number variant analysis</h1>
<ul>
<li> Joint SNP and CNV tests for common copy number variants
<li> Filtering and summary procedures for segmental (rare) CNV data
<li> Case/control comparison tests for global CNV properties
<li> Permutation-based association procedure for identifying specific loci
</ul>
<h1> Additional tests</h1>
<ul>
<li> Gene-based tests of association
<li> Screen for epistasis
<li> Gene-environment interaction with continuous and dichotomous environments
</ul>
<h1>Meta-analysis</h1>
<ul>
<li> Automatically combine several generically-formatted summary files, for millions of SNPs
<li> Fixed and random effects models
</ul>
<h1>Result annotation and reporting</h1>
<ul>
<li> Post-analysis annotation of result files
<li> LD-based and region-based grouping of results across multiple studies
</ul>
<h1> Additional features</h1>
<ul>
<li> Extensible with via R function plug-ins
<li> Web-based SNP and gene annotation lookup feature
<li> Simple SNP simulation feature
<li> ID helper tools, for tracking and working with project data
<li> See the main documentation for full list of features
</ul>
</td>
<td width=5%> </td>
</tr>
</table>
<hr>
<em>
This document last modified Friday, 29-Jun-2018 20:09:27 CDT
</em><
</body>
<HEAD>
<META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE">
</HEAD>
</html>