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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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Warnings & Known Issues
Development of PLINK is ongoing: as such, there is always
likely to be a list of features that are only partialy implemented, or
have problems of some kind. Our policy is to release a web-based
warning for these as soon as any problems are identified, and, for
more major problems, to release a patched version on the main download
page as soon as possible.
Note that any new patched verions will still give the web-based
warning message (i.e. that is based solely on version number, rather
than patch).
Want to ignore a warning and run the analysis anyway? Then run
PLINK with the --noweb flag to disable the web-check. Not
recommended...
Often, the issues flagged here are fixed in the development source
code, available from , which
you will need to compile yourself.
Format issue with --hardy option
Date: Sep 1 2008
Version: 1.04
Problem: The output of the --hardy command has the fields in
the wrong order, with the TEST and A1, A2 fields
swapped. Also, the A2 field always equal the A1. This is
fixed in development source code available online; will be fixed in
next release
Problem with --chap and missing genotype data
Date: Oct 20 2008
Version: 1.04
Problem: A serious problem emerged with the conditional
haplotype tests: when there is a reasonable amount of missing genotype
data, the p-values calculated can be very liberal. This is because
individuals were included under the null model likelihood calculations
but not the alternate model calculations under these scenarios. Fixed
in development source code; will be fixed in next release. As an
approximate, temporary fix, add the option --hap-miss 2 (this
will mean that all individuals are phased and included in the test, no
matter how much missing genotype data they have)
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