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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. Multimarker tests
15. Conditional haplotype tests
16. Proxy association
17. Full imputation (beta)
18. LD-based results clumping
19. Epistasis
20. Copy Number Variation
21. R-plugins
22. SNP annotation lookup
23. Simulation tools
24. Profile scoring
25. Resources
26. Miscellaneous
27. FAQ & Hints
28. 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 200 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 v1.03 PDF documentation (available soon)
PLINK v1.02 PDF documentation
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