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

Output modifiers

One convenient filter is

     --pfilter 1e-3

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)

     --log10

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

     --lambda 1.2

To obtain an extra set of columns that facilitates making a Q-Q plot in the *.adjusted file, add the option

     --qq-plot

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

     --dog
     --horse
     --cow
     --sheep
     --rice
     --mouse

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.

./plink --dog

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;

File compression

The options

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.

Known issues

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:

     http://zzz.bwh.harvard.edu/plink/warnings.shtml

This document last modified Wednesday, 25-Jan-2017 11:52:28 EST