Feb 01, 2016. The original version of PLINK will continue to be available for download at the original website. PLINK 1.9 is currently under heavy active development - users may wish to check certain results against the original PLINK (1.07) and notify the above list of any discrepancies. Download PuTTY for Windows operating system. Step by step guide to using SSH in PuTTY. Free download putty for Mac and Linux. Latest version Putty 0.73 is available here. GPLINK is a freely-available, Java-based software package that:. Is a GUI that allows construction of many common PLINK operations; provides a simple project management tool and analysis log allows for data and computation to be on a separate server (via SSH).
--help [flag name/prefix..]
When invoked with no parameters, --help provides a summary of all PLINK flags, starting with the main functions. This is long (over 1000 lines); we recommend you pipe the output through a terminal pager like Unix less or more, or dump it to a file with e.g.
plink --help > plink-help.txt
Canon image capture mac download. Alternatively, you can provide one or more flag names/prefixes to cause PLINK to only display information on the referenced flags, e.g.
[chrchang:~/plink-ng]$ plink --help abcd Z-gneome
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 --genome ['gz'] ['rel-check'] ['full'] ['unbounded'] ['nudge'] Generate an identity-by-descent report. * It is usually best to perform this calculation on a marker set in approximate linkage equilibrium. * The 'rel-check' modifier excludes pairs of samples with different FIDs from the final report. * 'full' adds raw pairwise comparison data to the report. * The P(IBD=0/1/2) estimator employed by this command sometimes yields numbers outside the range [0,1]; by default, these are clipped. The 'unbounded' modifier turns off this clipping. * Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2) estimates to a theoretically possible configuration. * The computation can be subdivided with --parallel. --ppc-gap <val> : Minimum number of base pairs, in thousands, between informative pairs of markers used in --genome PPC test. 500 if unspecified. --min <cutoff> : Specify minimum PI_HAT for inclusion in --genome report. --max <cutoff> : Specify maximum PI_HAT for inclusion in --genome report. No help entry for 'abcd'.
More precisely, for each parameter you pass to --help, PLINK will first search for an exact flag name match; if it fails to find one, it will then search for exact prefix matches; and if it also fails to find any of those, it will search for Damerau-Levenshtein distance 1 matches (note the 'Z-gneome' misspelling above). (The 'Quick index search' on this webpage's sidebar uses the same logic.)
Plink V1.9
If --help is used with other flags (other than --script and --rerun), it causes everything before it on the command line to be ignored, and everything after it to be treated as --help parameters. This is convenient when you've forgotten exactly how a flag works while in the middle of typing a long command: you can put your help request at the end of the unfinished command, and then retrieve your unfinished command line with the up arrow (in most shells, anyway).
[chrchang:~/plink-ng]$ plink --bfile test_data --hwe 1e-5 midp --help --pca
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 --help present, ignoring other flags. --pca {count} ['header'] ['tabs'] ['var-wts'] Calculates a variance-standardized relationship matrix (use --make-rel/--make-grm-gz/--make-grm-bin to dump it), and extracts the top 20 principal components. * It is usually best to perform this calculation on a marker set in approximate linkage equilibrium. * You can change the number of PCs by passing a numeric parameter. * The 'header' modifier adds a header line to the .eigenvec output file. (For compatibility with the GCTA flag of the same name, the default is no header line.) * The 'tabs' modifier causes the .eigenvec file(s) to be tab-delimited. * The 'var-wts' modifier requests an additional .eigenvec.var file with PCs expressed as variant weights instead of sample weights. --pca-cluster-names <..> : These can be used individually or in combination --pca-clusters <fname> to define a list of clusters to use in the basic --pca computation. (--pca-cluster-names expects a space-delimited sequence of cluster names, while --pca-clusters expects a file with one cluster name per line.) All samples outside those clusters will then be projected on to the calculated PCs. [chrchang:~/plink-ng]$ plink --bfile test_data --hwe 1e-5 midp --pca .. Download Plink For WindowsGetting started
After downloading and unzipping PLINK 1.9, you should see the main PLINK 1.9 binary, the GPLv3 license, the prettify utility for generating clean space-delimited text tables, and the small files toy.ped and toy.map. Try the command
./plink --file toy --freq --out toy_analysis
You should see something like:
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to toy_analysis.log. Options in effect: --file toy --freq --out toy_analysis 4096 MB RAM detected; reserving 2048 MB for main workspace. .ped scan complete (for binary autoconversion). Performing single-pass .bed write (2 variants, 2 people). --file: toy_analysis-temporary.bed + toy_analysis-temporary.bim + toy_analysis-temporary.fam written. 2 variants loaded from .bim file. 2 people (2 males, 0 females) loaded from .fam. 2 phenotype values loaded from .fam. Using 1 thread (no multithreaded calculations invoked). Calculating allele frequencies.. done. Total genotyping rate is 0.75. --freq: Allele frequencies (founders only) written to toy_analysis.frq .
(If it fails, you might have downloaded the wrong package for your machine. Double-check the Downloads table; if you're still stumped, our plink2-users Google group may help.)
Okay, what did my command mean? And what just happened?
PLINK 1.9 parses each command line as a collection of flags (each of which starts with two dashes1), plus parameters (which immediately follow a flag, and never start with a dash unless that dash is immediately followed by a digit) for those flags. So the command above included three flags: --file, --freq, and --out. They specify the following three things, which are part of almost every PLINK run:
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So this particular combination makes PLINK calculate allele frequencies in toy.ped + toy.map, and write a report to toy_analysis.frq.
If you have PLINK 1.07 installed, try running the same command with it: you should get exactly the same report, down to the last byte. We are aiming for this level of concordance across almost all PLINK 1.07 commands where it might be wanted.
1: Actually, that was a lie. With the exceptions of --1 and --23file, PLINK 1.9 allows you to use a single dash in front of each flag. In exchange for saving you some keystrokes, please do yourself a favor and avoid filenames that begin with a dash.
2: PLINK 1.9 is usually less strict than PLINK 1.07 when it comes to allowing multiple calculations in a single run. See the order of operations page for details. Interpreting our flag usage summaries
The rest of this documentation has many one-line summaries describing the parameter sets accepted by particular flags, followed by discussions of flag functionality and the effects of optional parameters. We use the following conventions in our one-line usage summaries (these were adjusted in March 2019 to be more consistent with community norms):
Install Plink
If you're already familiar with PLINK, this should help you skim over stuff you already know. If there are just one or two flags you need to look up, you can quickly find what you need in the sidebar; try the search box if the correct page isn't immediately apparent.
For the newer bioinformaticians out there, here's our first full flag description.
Setting the output file prefix
--out <prefix>
By default, the output files generated by PLINK all have names of the form 'plink.<one of these extensions>'. Apple imessages app mac is gone. This is fine for a single run, but as soon as you make more use of PLINK, you'll start causing results from previous runs to be overwritten.
Therefore, you usually want to choose a different output file prefix for each run. --out causes 'plink' to be replaced with the prefix you provide. E.g. in the example above, '--out toy_analysis' caused PLINK to create a file named toy_analysis.frq instead of plink.frq.
Since the prefix is a required parameter, invoking --out without it will cause PLINK to quit during command line parsing:
[chrchang:~/plink-ng]$ ./plink --file toy --freq --out
PLINK v1.90b6.9 64-bit (4 Mar 2019) www.cog-genomics.org/plink/1.9/ (C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3 Error: Missing --out parameter. For more information, try 'plink --help <flag name>' or 'plink --help | more'.
In the rest of this documentation, we will continue highlighting full command lines in purple, default parameter values in orange, and sample parameter values you can freely change in green.
Citation instructions
Adium for mac. If you use PLINK 1.9 in any published work, please cite both the software (as an electronic resource/URL):
Package : PLINK [version]
Authors : Shaun Purcell, Christopher Chang URL : www.cog-genomics.org/plink/1.9/
and the manuscript(s) describing the methods you used. Our primary methods paper is: Aol for mac. https://ameblo.jp/vicbabotheat1972/entry-12630798564.html.
Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4.
PLINK 1.9 includes implementations of many analyses that were developed by other teams. The original sources are summarized below.
Plink Software Download
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