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
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
22. LD-based results clumping
23. Gene-based report
25. Rare CNVs
26. Common CNPs
28. Annotation web-lookup
29. Simulation tools
30. Profile scoring
31. ID helper
35. FAQ & Hints
This page details a collection of options and commands that did not
get proper mention elsewhere.
Certain PLINK commands allow variable options to be passed,
in addition to the standard arguments. These typically modify the
behavior of the main command in some way. The basic syntax is:
--command arg1 arg2 option1 option2=value --next-command ...
In this example, the first --command takes two arguments,
arg1 and arg2. Here, this command allows for
additional options to be passed: for example, option1 and
option2=value. Options are either single keywords, or
key/value pairs. For example, the usual command to analyse dosage data,
only for a given chromosome, is
plink --dosage myfile.raw --chr 22
where --dosage expects a single argument. To pass an modifying option to the --dosage
command, it must be listed after the last fixed argument of the command, and before the next command, if any
(i.e. next command starting --). For example,
plink --dosage myfile.raw Zout --chr 22
will pass Zout as an option to the --dosage command
(this means that the output is written in compressed format, if ZLIB
support is present. Unlike normal commands, if options are not
recognised, they are simply ignored (i.e. no error message is given).
For some options that take a variable number of arguments
(e.g. --meta-analysis) it is necessary to use a plus
symbol to distinguish between the arguments and any options.
--command arg1 arg2 + option1 option2=value --next-command ...
For example, a possible option for --meta-analysis is
qt, to indicate that the summary statistics are for
quantitative trait analyses:
./plink --meta-analysis file1.qassoc file2.qassoc file3.assoc.linear + qt
One convenient filter is
which will, for example, only report statistics with p-values less than 1e-3.
NOTE This is operation for the basic association
tests, but do not expect this to work for all methods that return a p-value.
To obtain -log10(p) values instead of p-values in the *adjusted file, add the
flag (this does not change the output of p-values in other files)
To fix the value of lambda used for the genomic control in
the *adjusted file, instead of estimating it from the data, use the
option, for example
To obtain an extra set of columns that facilitates making a Q-Q plot
in the *.adjusted file, add the option
This will work with either basic p-values, or with --log10 p-values.
Analyses with different species
PLINK differentiates between species only in terms of the number of
chromosomes and which are sex-linked or haploid. Several non-human
species are supported, by adding one of the following flags
NOTE This flag needs to be added to every analysis. If you work primarily
with one of these non-human species, you might want to make a link or wrapper to make, e.g.
myplink always add the flag, e.g.
or compile PLINK with the option fixed (in options.cpp, edit the appropriate line, by setting one of these to true:
bool par::species_dog = false;
bool par::species_cow = false;
bool par::species_horse = false;
bool par::species_sheep = false;
bool par::species_rice = false;
plink --compress myfile
will compress a file (applying gzip compression, if the ZLIB support
is available for PLINK). The command
plink --decompress myfile.gz
will decompres that file, but by default generating a new file.
Development of PLINK is ongoing: as such, there is always
likely to be a list of features, listed here, that are only partialy
implemented, or have known problems not yet fixed. A list of known issues
can be found on the warnings page: