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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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New features / under development
This page lists the features that have just been added to the
development source code (i.e. and are not yet in the stable release).
IMPORTANT Unless you know what you are doing, you are
best to ignore this page and these features until they feature in the
stable release and are documented in the main website.
- Added --cnv-test-region command
- Fixed minor bug in haplotyping routine that could cause a segfault when a haplotype of size 1 SNP is phased
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