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.
Posted in News, Putty for Mac Tagged faq, mac, mac osx, macos, pageant, plink, putty, Putty for Mac, puttygen, telnet, terminal emulator Leave a comment Putty for Mac version 9.0 status update Posted on July 24, 2017 by WinOnMacs. I've downloaded the newer PLINK version 1.9 and it's working perfectly. Wishes, ADD REPLY. link written 11 weeks ago by husainalsaleh79. 0. I tried to use Plink on Mac. I was able to successfully download and unzip the profile from 'http. Strand Specific Tophat Output. May 28, 2020. . PLINK is available for Linux, Mac OS, and MS-DOS. PLINK has 2 versions, the stable version (1.07) and the beta version (1.9) – PLINK 1.9 works much faster than 1.07 – PLINK 1.9 has many new features. gPLINK is the other version of PLINK that provides graphical user interface.
plink --help > plink-help.txt
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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'. Mac desktop icons download.
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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 1.9 Manual
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).
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[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 ..