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1. Introduction
2. Basic information
3. Download and general notes
4. Command reference table
5. Basic usage/data formats
6. Data management
7. Summary stats
8. Inclusion thresholds
9. Population stratification
10. IBS/IBD estimation
11. Association
12. Family-based association
13. Permutation procedures
14. LD calculations
15. Multimarker tests
16. Conditional haplotype tests
17. Proxy association
18. Imputation (beta)
19. Dosage data
20. Meta-analysis
21. Annotation
22. LD-based results clumping
23. Gene-based report
24. Epistasis
25. Rare CNVs
26. Common CNPs
27. R-plugins
28. Annotation web-lookup
29. Simulation tools
30. Profile scoring
31. ID helper
32. Resources
33. Flow-chart
34. Miscellaneous
35. FAQ & Hints
36. gPLINK
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PDF version of web documentation
A PDF version of this website is available for download. Please note:
it is automatically generated from the notes on these webpages, and so
not all characters and formatting have been completely preserved.
Also, it is almost 300 pages long, so please consider this before
printing. Also please consider that the web is updated fairly
regularly, inbetween major version releases, so any printed PDF will
soon become redundant.
PLINK v1.07 PDF documentation
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