Command-line help
--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 1500 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.
plink2 --help > plink2-help.txt
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]$ plink2 --help abcd gneome
PLINK v2.00a4 AVX2 (1 Jan 2023) www.cog-genomics.org/plink/2.0/
(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3
--make-king-table ['zs'] ['counts'] ['rel-check'] ['cols='<col set descrip.>]
Similar to --make-king, except results are reported in KING's original
.kin0 text table format (with minor changes, e.g. row order is more
friendly to incremental addition of samples), --king-table-filter can be
used to restrict the report to high kinship values, and the 'rel-check'
modifier can be used to restrict to same-FID pairs.
Supported column sets are:
maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
fid: Force FID1/FID2 even when FID was absent in the input.
id: IID1/IID2.
maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
sid: Force SID1/SID2 even when SID was absent in the input.
nsnp: Number of variants considered (autosomal, neither call missing).
hethet: Proportion/count of considered call pairs which are het-het.
ibs0: Proportion/count of considered call pairs which are opposite homs.
ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.
kinship: KING-robust between-family kinship estimator.
The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.
hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is
present. If id is omitted, a .kin0.id file is also written.
No help entry for 'abcd'.
More precisely, for each parameter you pass to --help, PLINK will first search for an exact flag name or keyword 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 'gneome' misspelling above; 'genome' is a keyword for --make-king-table, since --make-king-table includes much of the functionality of PLINK 1.x's --genome command).
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]$ plink2 --pfile test_data --hwe 1e-10 midp keep-fewhet --help --pca
PLINK v2.00a4 AVX2 (1 Jan 2023) www.cog-genomics.org/plink/2.0/
(C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3
--help present, ignoring other flags.
--pca [count] [{approx | meanimpute}] ['scols='<col set descriptor>]
--pca [{allele-wts | biallelic-var-wts}] [count] [{approx | meanimpute}]
['vzs'] ['scols='<col set descriptor>] ['vcols='<col set descriptor>]
Extracts top principal components from the variance-standardized
relationship matrix.
* It is usually best to perform this calculation on a variant set in
approximate linkage equilibrium, with no very-low-MAF variants.
* By default, 10 PCs are extracted; you can adjust this by passing a
numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of
20; this is due to the randomized algorithm's memory footprint growing
quadratically w.r.t. the PC count.)
* The 'approx' modifier causes the standard deterministic computation to be
replaced with the randomized algorithm originally implemented for
Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,
Price AL (2016) Fast Principal-Component Analysis Reveals Convergent
Evolution of ADH1B in Europe and East Asia. This can be a good idea when
you have >5k samples, and is almost required with >50k.
* The randomized algorithm always uses mean imputation for missing genotype
calls. For comparison purposes, you can use the 'meanimpute' modifier to
request this behavior for the standard computation.
* 'scols=' can be used to customize how sample IDs appear in the .eigenvec
file. (maybefid, fid, maybesid, and sid supported; default is
maybefid,maybesid.)
* The 'allele-wts' modifier requests an additional one-line-per-allele
.eigenvec.allele file with PCs expressed as allele weights instead of
sample weights. When it's present, 'vzs' causes the .eigenvec.allele
file to be Zstd-compressed.
'vcols=' can be used to customize the report columns; supported column
sets are:
chrom: Chromosome ID.
pos: Base-pair coordinate.
(ID is always present, and positioned here.)
ref: Reference allele.
alt1: Alternate allele 1.
alt: All alternate alleles, comma-separated.
(A1 is always present, and positioned here.)
ax: Non-A1 alleles, comma-separated.
(PCs are always present, and positioned here.)
Default is chrom,ref,alt.
* For datasets with no multiallelic variants, the 'biallelic-var-wts'
modifier requests the old .eigenvec.var format, which only reports
weights for major alleles. (These weights are 2x the corresponding
.eigenvec.allele weights.) Supported column sets are:
chrom: Chromosome ID.
pos: Base-pair coordinate.
(ID is always present, and positioned here.)
ref: Reference allele.
alt1: Alternate allele 1.
alt: All alternate alleles, comma-separated.
maj: Major allele.
nonmaj: All nonmajor alleles, comma-separated.
(PCs are always present, and positioned here. Signs are w.r.t. the
major, not necessarily reference, allele.)
Default is chrom,maj,nonmaj.
[chrchang:~/plink-ng]$ plink2 --pfile test_data
--hwe 1e-10 midp keep-fewhet --pca ...
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