[med-svn] [Git][med-team/plink1-9][master] Do not generate manpage with help2man
Dylan Aïssi
gitlab at salsa.debian.org
Tue Apr 21 10:00:07 BST 2020
Dylan Aïssi pushed to branch master at Debian Med / plink1.9
Commits:
391c3a96 by Dylan Aïssi at 2020-04-21T10:59:13+02:00
Do not generate manpage with help2man
- - - - -
3 changed files:
- debian/control
- + debian/plink1.9.1
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -4,7 +4,6 @@ Uploaders: Dylan Aïssi <daissi at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
- help2man,
libatlas-base-dev,
liblapack-dev,
zlib1g-dev
=====================================
debian/plink1.9.1
=====================================
@@ -0,0 +1,2512 @@
+.TH PLINK "1" "March 2020" "PLINK v1.90b6.16 64-bit (19 Feb 2020)" "User Commands"
+.SH NAME
+PLINK \- whole genome SNP analysis
+.SH DESCRIPTION
+PLINK v1.90b6.16 64\-bit (19 Feb 2020) www.cog\-genomics.org/plink/1.9/
+(C) 2005\-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
+.PP
+In the command line flag definitions that follow,
+.IP
+* <angle brackets> denote a required parameter, where the text between the
+.IP
+angle brackets describes its nature.
+.TP
+* ['square brackets + single\-quotes'] denotes an optional modifier.
+Use the
+.IP
+EXACT text in the quotes.
+.IP
+* [{bar|separated|braced|bracketed|values}] denotes a collection of mutually
+.TP
+exclusive optional modifiers (again, the exact text must be used).
+When
+.IP
+there are no outer square brackets, one of the choices must be selected.
+.IP
+* ['quoted_text='<description of value>] denotes an optional modifier that
+.IP
+must begin with the quoted text, and be followed by a value with no
+whitespace in between. '|' may also be used here to indicate mutually
+exclusive options.
+.IP
+* [square brackets without quotes or braces] denote an optional parameter,
+.IP
+where the text between the brackets describes its nature.
+.IP
+* An ellipsis (...) indicates that you may enter multiple parameters of the
+.IP
+specified type.
+.IP
+plink <input flag(s)...> [command flag(s)...] [other flag(s)...]
+plink \fB\-\-help\fR [flag name(s)...]
+.PP
+Most PLINK runs require exactly one main input fileset. The following flags
+are available for defining its form and location:
+.HP
+\fB\-\-bfile\fR [prefix] : Specify .bed + .bim + .fam prefix (default 'plink').
+.HP
+\fB\-\-bed\fR <filename> : Specify full name of .bed file.
+.HP
+\fB\-\-bim\fR <filename> : Specify full name of .bim file.
+.HP
+\fB\-\-fam\fR <filename> : Specify full name of .fam file.
+.TP
+\fB\-\-keep\-autoconv\fR
+: With \fB\-\-file\fR/\-\-tfile/\-\-lfile/\-\-vcf/\-\-bcf/\-\-data/\-\-23file,
+don't delete autogenerated binary fileset at end of run.
+.TP
+\fB\-\-file\fR [prefix]
+: Specify .ped + .map filename prefix (default 'plink').
+.HP
+\fB\-\-ped\fR <filename> : Specify full name of .ped file.
+.HP
+\fB\-\-map\fR <filename> : Specify full name of .map file.
+.TP
+\fB\-\-no\-fid\fR
+: .fam/.ped file does not contain column 1 (family ID).
+.TP
+\fB\-\-no\-parents\fR
+: .fam/.ped file does not contain columns 3\-4 (parents).
+.TP
+\fB\-\-no\-sex\fR
+: .fam/.ped file does not contain column 5 (sex).
+.TP
+\fB\-\-no\-pheno\fR
+: .fam/.ped file does not contain column 6 (phenotype).
+.HP
+\fB\-\-tfile\fR [prefix] : Specify .tped + .tfam filename prefix (default 'plink').
+.TP
+\fB\-\-tped\fR <fname>
+: Specify full name of .tped file.
+.TP
+\fB\-\-tfam\fR <fname>
+: Specify full name of .tfam file.
+.HP
+\fB\-\-lfile\fR [prefix] : Specify .lgen + .map + .fam (long\-format fileset) prefix.
+.TP
+\fB\-\-lgen\fR <fname>
+: Specify full name of .lgen file.
+.HP
+\fB\-\-reference\fR <fn> : Specify default allele file accompanying .lgen input.
+.TP
+\fB\-\-allele\-count\fR
+: When used with \fB\-\-lfile\fR/\-\-lgen + \fB\-\-reference\fR, specifies
+that the .lgen file contains reference allele counts.
+.HP
+\fB\-\-vcf\fR <filename> : Specify full name of .vcf or .vcf.gz file.
+.HP
+\fB\-\-bcf\fR <filename> : Specify full name of BCF2 file.
+.TP
+\fB\-\-data\fR [prefix]
+: Specify Oxford .gen + .sample prefix (default 'plink').
+.HP
+\fB\-\-gen\fR <filename> : Specify full name of .gen or .gen.gz file.
+.HP
+\fB\-\-bgen\fR <f> ['snpid\-chr'] : Specify full name of .bgen file.
+.HP
+\fB\-\-sample\fR <fname> : Specify full name of .sample file.
+.HP
+\fB\-\-23file\fR <fname> [FID] [IID] [sex] [pheno] [pat. ID] [mat. ID] :
+.IP
+Specify 23andMe input file.
+.TP
+\fB\-\-grm\-gz\fR [prfx]
+: Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix.
+.TP
+\fB\-\-grm\-bin\fR [prfx] : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular
+binary relationship matrix) filename prefix.
+.HP
+\fB\-\-dummy\fR <sample ct> <SNP ct> [missing geno freq] [missing pheno freq]
+.IP
+[{acgt | 1234 | 12}] ['scalar\-pheno']
+.IP
+This generates a fake input dataset with the specified number of samples
+and SNPs. By default, the missing genotype and phenotype frequencies are
+zero, and genotypes are As and Bs (change the latter with
+\&'acgt'/'1234'/'12'). The 'scalar\-pheno' modifier causes a normally
+distributed scalar phenotype to be generated instead of a binary one.
+.HP
+\fB\-\-simulate\fR <simulation parameter file> [{tags | haps}] [{acgt | 1234 | 12}]
+.HP
+\fB\-\-simulate\-qt\fR <sim. parameter file> [{tags | haps}] [{acgt | 1234 | 12}]
+.HP
+\fB\-\-simulate\fR generates a fake input dataset with disease\-associated SNPs,
+.IP
+while \fB\-\-simulate\-qt\fR generates a dataset with quantitative trait loci.
+.PP
+Output files have names of the form 'plink.<extension>' by default. You can
+change the 'plink' prefix with
+.TP
+\fB\-\-out\fR <prefix>
+: Specify prefix for output files.
+.PP
+Most runs also require at least one of the following commands:
+.HP
+\fB\-\-make\-bed\fR
+.TP
+Create a new binary fileset.
+Unlike the automatic text\-to\-binary
+.IP
+converters (which only heed chromosome filters), this supports all of
+PLINK's filtering flags.
+.HP
+\fB\-\-make\-just\-bim\fR
+.HP
+\fB\-\-make\-just\-fam\fR
+.TP
+Variants of \fB\-\-make\-bed\fR which only write a new .bim or .fam file..
+Can be
+.IP
+used with only .bim/.fam input.
+USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary
+genotype data and your .bim/.fam indexes if you use these commands
+improperly. If you have any doubt, stick with \fB\-\-make\-bed\fR.
+.HP
+\fB\-\-recode\fR <output format> [{01 | 12}] [{tab | tabx | spacex | bgz | gen\-gz}]
+.IP
+['include\-alt'] ['omit\-nonmale\-y']
+.TP
+Create a new text fileset with all filters applied.
+The following output
+.IP
+formats are supported:
+* '23': 23andMe 4\-column format. This can only be used on a single
+.IP
+sample's data (\fB\-\-keep\fR may be handy), and does not support multicharacter
+allele codes.
+.IP
+* 'A': Sample\-major additive (0/1/2) coding, suitable for loading from R.
+.IP
+If you need uncounted alleles to be named in the header line, add the
+\&'include\-alt' modifier.
+.IP
+* 'AD': Sample\-major additive (0/1/2) + dominant (het=1/hom=0) coding.
+.IP
+Also supports 'include\-alt'.
+.IP
+* 'A\-transpose': Variant\-major 0/1/2.
+* 'beagle': Unphased per\-autosome .dat and .map files, readable by early
+.IP
+BEAGLE versions.
+.IP
+* 'beagle\-nomap': Single .beagle.dat file.
+* 'bimbam': Regular BIMBAM format.
+* 'bimbam\-1chr': BIMBAM format, with a two\-column .pos.txt file. Does not
+.IP
+support multiple chromosomes.
+.IP
+* 'fastphase': Per\-chromosome fastPHASE files, with
+.IP
+\&.chr\-<chr #>.recode.phase.inp filename extensions.
+.TP
+* 'fastphase\-1chr': Single .recode.phase.inp file.
+Does not support
+.IP
+multiple chromosomes.
+.IP
+* 'HV': Per\-chromosome Haploview files, with .chr\-<chr #>{.ped,.info}
+.IP
+filename extensions.
+.TP
+* 'HV\-1chr': Single Haploview .ped + .info file pair.
+Does not support
+.IP
+multiple chromosomes.
+.IP
+* 'lgen': PLINK 1 long\-format (.lgen + .fam + .map), loadable with \fB\-\-lfile\fR.
+* 'lgen\-ref': .lgen + .fam + .map + .ref, loadable with \fB\-\-lfile\fR +
+.HP
+\fB\-\-reference\fR.
+.TP
+* 'list': Single genotype\-based list, up to 4 lines per variant.
+To omit
+.IP
+nonmale genotypes on the Y chromosome, add the 'omit\-nonmale\-y' modifier.
+.IP
+* 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a
+.IP
+genotype\-based list which omits the most common genotype for each
+variant. Also supports 'omit\-nonmale\-y'.
+.TP
+* 'oxford': Oxford\-format .gen + .sample.
+With the 'gen\-gz' modifier, the
+.IP
+\&.gen file is gzipped.
+.IP
+* 'ped': PLINK 1 sample\-major (.ped + .map), loadable with \fB\-\-file\fR.
+* 'compound\-genotypes': Same as 'ped', except that the space between each
+.IP
+pair of same\-variant allele codes is removed.
+.IP
+* 'structure': Structure\-format.
+* 'transpose': PLINK 1 variant\-major (.tped + .tfam), loadable with
+.HP
+\fB\-\-tfile\fR.
+.TP
+* 'vcf', 'vcf\-fid', 'vcf\-iid': VCFv4.2.
+\&'vcf\-fid' and 'vcf\-iid' cause
+.IP
+family IDs or within\-family IDs respectively to be used for the sample
+IDs in the last header row, while 'vcf' merges both IDs and puts an
+underscore between them. If the 'bgz' modifier is added, the VCF file is
+block\-gzipped.
+The A2 allele is saved as the reference and normally flagged as not based
+on a real reference genome (INFO:PR). When it is important for reference
+alleles to be correct, you'll also want to include \fB\-\-a2\-allele\fR and
+\fB\-\-real\-ref\-alleles\fR in your command.
+.IP
+In addition,
+* The '12' modifier causes A1 (usually minor) alleles to be coded as '1'
+.IP
+and A2 alleles to be coded as '2', while '01' maps A1 \-> 0 and A2 \-> 1..
+.IP
+* The 'tab' modifier makes the output mostly tab\-delimited instead of
+.TP
+mostly space\-delimited.
+\&'tabx' and 'spacex' force all tabs and all
+.IP
+spaces, respectively.
+.HP
+\fB\-\-flip\-scan\fR ['verbose']
+.IP
+(alias: \fB\-\-flipscan\fR)
+LD\-based scan for case/control strand inconsistency.
+.HP
+\fB\-\-write\-covar\fR
+.IP
+If a \fB\-\-covar\fR file is loaded, \fB\-\-make\-bed\fR/\-\-make\-just\-fam and \fB\-\-recode\fR
+automatically generate an updated version (with all filters applied).
+However, if you do not wish to simultaneously generate a new genotype file,
+you can use \fB\-\-write\-covar\fR to just produce a pruned covariate file.
+.HP
+\fB\-\-write\-cluster\fR ['omit\-unassigned']
+.IP
+If clusters are specified with \fB\-\-within\fR/\-\-family, this generates a new
+cluster file (with all filters applied). The 'omit\-unassigned' modifier
+causes unclustered samples to be omitted from the file; otherwise their
+cluster is 'NA'.
+.HP
+\fB\-\-write\-set\fR
+.HP
+\fB\-\-set\-table\fR
+.IP
+If sets have been defined, \fB\-\-write\-set\fR dumps 'END'\-terminated set
+membership lists to <output prefix>.set, while \fB\-\-set\-table\fR writes a
+variant\-by\-set membership table to <output prefix>.set.table.
+.HP
+\fB\-\-merge\fR <.ped filename> <.map filename>
+.HP
+\fB\-\-merge\fR <text fileset prefix>
+.HP
+\fB\-\-bmerge\fR <.bed filename> <.bim filename> <.fam filename>
+.HP
+\fB\-\-bmerge\fR <binary fileset prefix>
+.IP
+Merge the given fileset with the initially loaded fileset, writing the
+result to <output prefix>.bed + .bim + .fam. (It is no longer necessary to
+simultaneously specify \fB\-\-make\-bed\fR.)
+.HP
+\fB\-\-merge\-list\fR <filename>
+.IP
+Merge all filesets named in the text file with the reference fileset, if
+one was specified. (However, this can also be used *without* a reference;
+in that case, the newly created fileset is then treated as the reference by
+most other PLINK operations.) The text file is interpreted as follows:
+* If a line contains only one name, it is assumed to be the prefix for a
+.IP
+binary fileset.
+.IP
+* If a line contains exactly two names, they are assumed to be the full
+.IP
+filenames for a text fileset (.ped first, then .map).
+.IP
+* If a line contains exactly three names, they are assumed to be the full
+.IP
+filenames for a binary fileset (.bed, then .bim, then .fam).
+.HP
+\fB\-\-write\-snplist\fR
+.HP
+\fB\-\-list\-23\-indels\fR
+.HP
+\fB\-\-write\-snplist\fR writes a .snplist file listing the names of all variants
+.IP
+which pass the filters and inclusion thresholds you've specified, while
+\fB\-\-list\-23\-indels\fR writes the subset with 23andMe\-style indel calls (D/I
+allele codes).
+.HP
+\fB\-\-list\-duplicate\-vars\fR ['require\-same\-ref'] ['ids\-only'] ['suppress\-first']
+.HP
+\fB\-\-list\-duplicate\-vars\fR writes a .dupvar file describing all groups of
+.IP
+variants with matching positions and allele codes.
+* By default, A1/A2 allele assignments are ignored; use 'require\-same\-ref'
+.IP
+to override this.
+.TP
+* Normally, the report contains position and allele codes.
+To remove them
+.IP
+(and produce a file directly usable with e.g. \fB\-\-extract\fR/\-\-exclude), use
+\&'ids\-only'. Note that this command will fail in 'ids\-only' mode if any
+of the reported IDs are not unique.
+.IP
+* 'suppress\-first' causes the first variant ID in each group to be omitted
+.IP
+from the report.
+.HP
+\fB\-\-freq\fR [{counts | case\-control}] ['gz']
+.HP
+\fB\-\-freqx\fR ['gz']
+.HP
+\fB\-\-freq\fR generates a basic allele frequency (or count, if the 'counts'
+.TP
+modifier is present) report.
+This can be combined with \fB\-\-within\fR/\-\-family
+.IP
+to produce a cluster\-stratified allele frequency/count report instead, or
+the 'case\-control' modifier to report case and control allele frequencies
+separately.
+\fB\-\-freqx\fR generates a more detailed genotype count report, designed for use
+with \fB\-\-read\-freq\fR.
+.HP
+\fB\-\-missing\fR ['gz']
+.TP
+Generate sample\- and variant\-based missing data reports.
+If clusters are
+.TP
+defined, the variant\-based report is cluster\-stratified.
+\&'gz' causes the
+.IP
+output files to be gzipped.
+Unlike most other commands, this doesn't treat het. haploids as missing.
+.HP
+\fB\-\-test\-mishap\fR
+.IP
+Check for association between missing calls and flanking haplotypes.
+.HP
+\fB\-\-hardy\fR ['midp'] ['gz']
+.TP
+Generate a Hardy\-Weinberg exact test p\-value report.
+(This does NOT
+.TP
+simultaneously filter on the p\-value any more; use \fB\-\-hwe\fR for that.)
+With
+.IP
+the 'midp' modifier, the test applies the mid\-p adjustment described in
+Graffelman J, Moreno V (2013) The mid p\-value in exact tests for
+Hardy\-Weinberg Equilibrium.
+.HP
+\fB\-\-mendel\fR ['summaries\-only']
+.TP
+Generate a Mendel error report.
+The 'summaries\-only' modifier causes the
+.IP
+\&.mendel file (listing every single error) to be skipped.
+.HP
+\fB\-\-het\fR ['small\-sample'] ['gz']
+.HP
+\fB\-\-ibc\fR
+.TP
+Estimate inbreeding coefficients.
+\fB\-\-het\fR reports method\-of\-moments
+.IP
+estimates, while \fB\-\-ibc\fR calculates all three values described in Yang J, Lee
+SH, Goddard ME and Visscher PM (2011) GCTA: A Tool for Genome\-wide Complex
+Trait Analysis. (That paper also describes the relationship matrix
+computation we reimplement.)
+* These functions require decent MAF estimates. If there are very few
+.IP
+samples in your immediate fileset, \fB\-\-read\-freq\fR is practically mandatory
+since imputed MAFs are wildly inaccurate in that case.
+.IP
+* They also assume the marker set is in approximate linkage equilibrium.
+* By default, \fB\-\-het\fR omits the n/(n\-1) multiplier in Nei's expected
+.TP
+homozygosity formula.
+The 'small\-sample' modifier causes it to be
+.IP
+included, while forcing \fB\-\-het\fR to use MAFs imputed from founders in the
+immediate dataset.
+.HP
+\fB\-\-check\-sex\fR [female max F] [male min F]
+.TP
+\fB\-\-check\-sex\fR ycount [female max F] [male min F] [female max Y obs]
+[male min Y obs]
+.HP
+\fB\-\-check\-sex\fR y\-only [female max Y obs] [male min Y obs]
+.HP
+\fB\-\-impute\-sex\fR [female max F] [male min F]
+.TP
+\fB\-\-impute\-sex\fR ycount [female max F] [male min F] [female max Y obs]
+[male min Y obs]
+.HP
+\fB\-\-impute\-sex\fR y\-only [female max Y obs] [male min Y obs]
+.HP
+\fB\-\-check\-sex\fR normally compares sex assignments in the input dataset with
+.IP
+those imputed from X chromosome inbreeding coefficients.
+* Make sure that the X chromosome pseudo\-autosomal region has been split
+.IP
+off (with e.g. \fB\-\-split\-x\fR) before using this.
+.IP
+* You also need decent MAF estimates (so, with very few samples in your
+.IP
+immediate fileset, use \fB\-\-read\-freq\fR), and your marker set should be in
+approximate linkage equilibrium.
+.IP
+* By default, F estimates smaller than 0.2 yield female calls, and values
+.TP
+larger than 0.8 yield male calls.
+If you pass numeric parameter(s) to
+.HP
+\fB\-\-check\-sex\fR, the first two control these thresholds.
+.IP
+There are now two modes which consider Y chromosome data.
+* In 'ycount' mode, gender is still imputed from the X chromosome, but
+.IP
+female calls are downgraded to ambiguous whenever more than 0 nonmissing
+Y genotypes are present, and male calls are downgraded when fewer than 0
+are present. (Note that these are counts, not rates.) These thresholds
+are controllable with \fB\-\-check\-sex\fR ycount's optional 3rd and 4th numeric
+parameters.
+.IP
+* In 'y\-only' mode, gender is imputed from nonmissing Y genotype counts..
+.IP
+The male minimum threshold defaults to 1 instead of zero in this case.
+.HP
+\fB\-\-impute\-sex\fR changes sex assignments to the imputed values, and is
+.TP
+otherwise identical to \fB\-\-check\-sex\fR.
+It must be used with
+.HP
+\fB\-\-make\-bed\fR/\-\-recode/\-\-write\-covar.
+.HP
+\fB\-\-fst\fR ['case\-control']
+.IP
+(alias: \fB\-\-Fst\fR)
+Estimate Wright's Fst for each autosomal diploid variant using the method
+introduced in Weir BS, Cockerham CC (1984) Estimating F\-statistics for the
+analysis of population structure, given a set of subpopulations defined via
+\fB\-\-within\fR. Raw and weighted global means are also reported.
+* If you're interested in the global means, it is usually best to perform
+.IP
+this calculation on a marker set in approximate linkage equilibrium.
+.IP
+* If you have only two subpopulations, you can represent them with
+.IP
+case/control status and use the 'case\-control' modifier.
+.HP
+\fB\-\-indep\fR <window size>['kb'] <step size (variant ct)> <VIF threshold>
+.HP
+\fB\-\-indep\-pairwise\fR <window size>['kb'] <step size (variant ct)> <r^2 threshold>
+.HP
+\fB\-\-indep\-pairphase\fR <window size>['kb'] <step size (variant ct)> <r^2 thresh>
+.TP
+Generate a list of markers in approximate linkage equilibrium.
+With the
+.IP
+\&'kb' modifier, the window size is in kilobase instead of variant count
+units. (Pre\-'kb' space is optional, i.e. "\-\-indep\-pairwise 500 kb 5 0.5"
+and "\-\-indep\-pairwise 500kb 5 0.5" have the same effect.)
+Note that you need to rerun PLINK using \fB\-\-extract\fR or \fB\-\-exclude\fR on the
+\&.prune.in/.prune.out file to apply the list to another computation.
+.HP
+\fB\-\-r\fR [{square | square0 | triangle | inter\-chr}] [{gz | bin | bin4}]
+.IP
+['spaces'] ['in\-phase'] [{d | dprime | dprime\-signed}] ['with\-freqs']
+['yes\-really']
+.HP
+\fB\-\-r2\fR [{square | square0 | triangle | inter\-chr}] [{gz | bin | bin4}]
+.IP
+['spaces'] ['in\-phase'] [{d | dprime | dprime\-signed}] ['with\-freqs']
+['yes\-really']
+.TP
+LD statistic reports.
+\fB\-\-r\fR yields raw inter\-variant correlations, while
+.TP
+\fB\-\-r2\fR reports their squares.
+You can request results for all pairs in
+.IP
+matrix format (if you specify 'bin' or one of the shape modifiers), all
+pairs in table format ('inter\-chr'), or a limited window in table format
+(default).
+* The 'gz' modifier causes the output text file to be gzipped.
+* 'bin' causes the output matrix to be written in double\-precision binary
+.TP
+format, while 'bin4' specifics single\-precision binary.
+The matrix is
+.IP
+square if no shape is explicitly specified.
+.IP
+* By default, text matrices are tab\-delimited; 'spaces' switches this.
+* 'in\-phase' adds a column with in\-phase allele pairs to table\-formatted
+.TP
+reports.
+(This cannot be used with very long allele codes.)
+.IP
+* 'dprime' adds the absolute value of Lewontin's D\-prime statistic to
+.IP
+table\-formatted reports, and forces both r/r^2 and D\-prime to be based on
+the maximum likelihood solution to the cubic equation discussed in Gaunt
+T, Rodriguez S, Day I (2007) Cubic exact solutions for the estimation of
+pairwise haplotype frequencies.
+\&'dprime\-signed' keeps the sign, while 'd' skips division by D_{max}.
+.IP
+* 'with\-freqs' adds MAF columns to table\-formatted reports.
+* Since the resulting file can easily be huge, you're required to add the
+.IP
+\&'yes\-really' modifier when requesting an unfiltered, non\-distributed all
+pairs computation on more than 400k variants.
+.IP
+* These computations can be subdivided with \fB\-\-parallel\fR (even when the
+.IP
+\&'square' modifier is active).
+.HP
+\fB\-\-ld\fR <variant ID> <variant ID> ['hwe\-midp']
+.IP
+This displays haplotype frequencies, r^2, and D' for a single pair of
+variants. When there are multiple biologically possible solutions to the
+haplotype frequency cubic equation, all are displayed (instead of just the
+maximum likelihood solution identified by \fB\-\-r\fR/\-\-r2), along with HWE exact
+test statistics.
+.HP
+\fB\-\-show\-tags\fR <filename>
+.HP
+\fB\-\-show\-tags\fR all
+.IP
+* If a file is specified, list all variants which tag at least one variant
+.TP
+named in the file.
+(This will normally be a superset of the original
+.IP
+list, since a variant is considered to tag itself here.)
+.IP
+* If 'all' mode is specified, for each variant, each *other* variant which
+.IP
+tags it is reported.
+.HP
+\fB\-\-blocks\fR ['no\-pheno\-req'] ['no\-small\-max\-span']
+.IP
+Estimate haplotype blocks, via Haploview's interpretation of the block
+definition suggested by Gabriel S et al. (2002) The Structure of Haplotype
+Blocks in the Human Genome.
+* Normally, samples with missing phenotypes are not considered by this
+.IP
+computation; the 'no\-pheno\-req' modifier lifts this restriction.
+.IP
+* Normally, size\-2 blocks may not span more than 20kb, and size\-3 blocks
+.TP
+are limited to 30kb.
+The 'no\-small\-max\-span' modifier removes these
+.IP
+limits.
+.TP
+The .blocks file is valid input for PLINK 1.07's \fB\-\-hap\fR command.
+However,
+.IP
+the \fB\-\-hap\fR... family of flags has not been reimplemented in PLINK 1.9 due to
+poor phasing accuracy relative to other software; for now, we recommend
+using BEAGLE instead of PLINK for case/control haplotype association
+analysis. (You can use "\-\-recode beagle" to export data to BEAGLE 3.3.)
+We apologize for the inconvenience, and plan to develop variants of the
+\fB\-\-hap\fR... flags which handle pre\-phased data effectively.
+.HP
+\fB\-\-distance\fR [{square | square0 | triangle}] [{gz | bin | bin4}] ['ibs']
+.IP
+['1\-ibs'] ['allele\-ct'] ['flat\-missing']
+.IP
+Write a lower\-triangular tab\-delimited table of (weighted) genomic
+distances in allele count units to <output prefix>.dist, and a list of the
+corresponding sample IDs to <output prefix>.dist.id. The first row of the
+\&.dist file contains a single <genome 1\-genome 2> distance, the second row
+has the <genome 1\-genome 3> and <genome 2\-genome 3> distances in that
+order, etc.
+* It is usually best to perform this calculation on a marker set in
+.IP
+approximate linkage equilibrium.
+.IP
+* If the 'square' or 'square0' modifier is present, a square matrix is
+.IP
+written instead; 'square0' fills the upper right triangle with zeroes.
+.IP
+* If the 'gz' modifier is present, a compressed .dist.gz file is written
+.IP
+instead of a plain text file.
+.IP
+* If the 'bin' modifier is present, a binary (square) matrix of
+.IP
+double\-precision floating point values, suitable for loading from R, is
+instead written to <output prefix>.dist.bin. ('bin4' specifies
+single\-precision numbers instead.) This can be combined with 'square0'
+if you still want the upper right zeroed out, or 'triangle' if you don't
+want to pad the upper right at all.
+.IP
+* If the 'ibs' modifier is present, an identity\-by\-state matrix is written
+.TP
+to <output prefix>.mibs.
+\&'1\-ibs' causes distances expressed as genomic
+.IP
+proportions (i.e. 1 \- IBS) to be written to <output prefix>.mdist.
+Combine with 'allele\-ct' if you want to generate the usual .dist file as
+well.
+.IP
+* By default, distance rescaling in the presence of missing genotype calls
+.IP
+is sensitive to allele count distributions: if variant A contributes, on
+average, twice as much to other pairwise distances as variant B, a
+missing call at variant A will result in twice as large of a missingness
+correction. To turn this off (because e.g. your missing calls are highly
+nonrandom), use the 'flat\-missing' modifier.
+.IP
+* The computation can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-distance\-matrix\fR
+.HP
+\fB\-\-ibs\-matrix\fR
+.IP
+These deprecated commands are equivalent to "\-\-distance 1\-ibs flat\-missing
+square" and "\-\-distance ibs flat\-missing square", respectively, except that
+they generate space\- instead of tab\-delimited text matrices.
+.HP
+\fB\-\-make\-rel\fR [{square | square0 | triangle}] [{gz | bin | bin4}]
+.IP
+[{cov | ibc2 | ibc3}]
+.IP
+Write a lower\-triangular variance\-standardized realized relationship matrix
+to <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.
+* It is usually best to perform this calculation on a marker set in
+.IP
+approximate linkage equilibrium.
+.IP
+* 'square', 'square0', 'triangle', 'gz', 'bin', and 'bin4' act as they do
+.IP
+on \fB\-\-distance\fR.
+.IP
+* The 'cov' modifier removes the variance standardization step, causing a
+.IP
+covariance matrix to be calculated instead.
+.IP
+* By default, the diagonal elements in the relationship matrix are based on
+.HP
+\fB\-\-ibc\fR's Fhat1; use the 'ibc2' or 'ibc3' modifiers to base them on Fhat2
+.IP
+or Fhat3 instead.
+.IP
+* The computation can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-make\-grm\-gz\fR ['no\-gz'] [{cov | ibc2 | ibc3}]
+.HP
+\fB\-\-make\-grm\-bin\fR [{cov | ibc2 | ibc3}]
+.HP
+\fB\-\-make\-grm\-gz\fR writes the relationships in GCTA's original gzipped list
+.IP
+format, which describes one pair per line, while \fB\-\-make\-grm\-bin\fR writes them
+in GCTA 1.1+'s single\-precision triangular binary format. Note that these
+formats explicitly report the number of valid observations (where neither
+sample has a missing call) for each pair, which is useful input for some
+scripts.
+These computations can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-rel\-cutoff\fR [val]
+.IP
+(alias: \fB\-\-grm\-cutoff\fR)
+Exclude one member of each pair of samples with relatedness greater than
+the given cutoff value (default 0.025). If no later operation will cause
+the list of remaining samples to be written to disk, this will save it to
+<output prefix>.rel.id.
+Note that maximizing the remaining sample size is equivalent to the NP\-hard
+maximum independent set problem, so we use a greedy algorithm instead of
+guaranteeing optimality. (Use the \fB\-\-make\-rel\fR and \fB\-\-keep\fR/\-\-remove flags if
+you want to try to do better.)
+.HP
+\fB\-\-ibs\-test\fR [permutation count]
+.HP
+\fB\-\-groupdist\fR [iters] [d]
+.IP
+Given case/control phenotype data, these commands consider three subsets of
+the distance matrix: pairs of affected samples, affected\-unaffected pairs,
+and pairs of unaffected samples. Each of these subsets has a distribution
+of pairwise genomic distances; \fB\-\-ibs\-test\fR uses permutation to estimate
+p\-values re: which types of pairs are most similar, while \fB\-\-groupdist\fR
+focuses on the differences between the centers of these distributions and
+estimates standard errors via delete\-d jackknife.
+.HP
+\fB\-\-regress\-distance\fR [iters] [d]
+.IP
+Linear regression of pairwise genomic distances on pairwise average
+phenotypes and vice versa, using delete\-d jackknife for standard errors. A
+scalar phenotype is required.
+* With less than two parameters, d is set to <number of people>^0.6 rounded
+.TP
+down.
+With no parameters, 100k iterations are run.
+.HP
+\fB\-\-regress\-rel\fR [iters] [d]
+.IP
+Linear regression of pairwise genomic relationships on pairwise average
+phenotypes, and vice versa. Defaults for iters and d are the same as for
+\fB\-\-regress\-distance\fR.
+.HP
+\fB\-\-genome\fR ['gz'] ['rel\-check'] ['full'] ['unbounded'] ['nudge']
+.IP
+Generate an identity\-by\-descent report.
+* It is usually best to perform this calculation on a marker set in
+.IP
+approximate linkage equilibrium.
+.IP
+* The 'rel\-check' modifier excludes pairs of samples with different FIDs
+.IP
+from the final report.
+.IP
+* 'full' adds raw pairwise comparison data to the report.
+* The P(IBD=0/1/2) estimator employed by this command sometimes yields
+.TP
+numbers outside the range [0,1]; by default, these are clipped.
+The
+.IP
+\&'unbounded' modifier turns off this clipping.
+.IP
+* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2)
+.IP
+estimates to a theoretically possible configuration.
+.IP
+* The computation can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-homozyg\fR [{group | group\-verbose}] ['consensus\-match'] ['extend']
+.IP
+['subtract\-1\-from\-lengths']
+.HP
+\fB\-\-homozyg\-snp\fR <min var count>
+.HP
+\fB\-\-homozyg\-kb\fR <min length>
+.HP
+\fB\-\-homozyg\-density\fR <max inverse density (kb/var)>
+.HP
+\fB\-\-homozyg\-gap\fR <max internal gap kb length>
+.HP
+\fB\-\-homozyg\-het\fR <max hets>
+.HP
+\fB\-\-homozyg\-window\-snp\fR <scanning window size>
+.HP
+\fB\-\-homozyg\-window\-het\fR <max hets in scanning window hit>
+.HP
+\fB\-\-homozyg\-window\-missing\fR <max missing calls in scanning window hit>
+.HP
+\fB\-\-homozyg\-window\-threshold\fR <min scanning window hit rate>
+.IP
+These commands request a set of run\-of\-homozygosity reports, and allow you
+to customize how they are generated.
+* If you're satisfied with all the default settings described below, just
+.TP
+use \fB\-\-homozyg\fR with no modifiers.
+Otherwise, \fB\-\-homozyg\fR lets you change a
+.IP
+few binary settings:
+* 'group[\-verbose]' adds a report on pools of overlapping runs of
+.TP
+homozygosity.
+(Automatically set when \fB\-\-homozyg\-match\fR is present.)
+.IP
+* With 'group[\-verbose]', 'consensus\-match' causes pairwise segmental
+.IP
+matches to be called based on the variants in the pool's consensus
+segment, rather than the variants in the pairwise intersection.
+.IP
+* Due to how the scanning window algorithm works, it is possible for a
+.TP
+reported ROH to be adjacent to a few homozygous variants.
+The 'extend'
+.IP
+modifier causes them to be included in the reported ROH if that
+wouldn't cause a violation of the \fB\-\-homozyg\-density\fR bound.
+.IP
+* By default, segment bp lengths are calculated as <end bp position> \-
+.TP
+<start bp position> + 1.
+Therefore, reports normally differ slightly
+.TP
+from PLINK 1.07, which does not add 1 at the end.
+For testing
+.IP
+purposes, you can use the 'subtract\-1\-from\-lengths' modifier to apply
+the old formula.
+.IP
+* By default, only runs of homozygosity containing at least 100 variants,
+.TP
+and of total length >= 1000 kilobases, are noted.
+You can change these
+.IP
+minimums with \fB\-\-homozyg\-snp\fR and \fB\-\-homozyg\-kb\fR, respectively.
+.IP
+* By default, a ROH must have at least one variant per 50 kb on average;
+.IP
+change this bound with \fB\-\-homozyg\-density\fR.
+.IP
+* By default, if two consecutive variants are more than 1000 kb apart, they
+.IP
+cannot be in the same ROH; change this bound with \fB\-\-homozyg\-gap\fR..
+.IP
+* By default, a ROH can contain an unlimited number of heterozygous calls;
+.IP
+you can impose a limit with \fB\-\-homozyg\-het\fR.
+.IP
+* By default, the scanning window contains 50 variants; change this with
+.HP
+\fB\-\-homozyg\-window\-snp\fR.
+.IP
+* By default, a scanning window hit can contain at most 1 heterozygous
+.IP
+call and 5 missing calls; change these limits with \fB\-\-homozyg\-window\-het\fR
+and \fB\-\-homozyg\-window\-missing\fR, respectively.
+.IP
+* By default, for a variant to be eligible for inclusion in a ROH, the hit
+.IP
+rate of all scanning windows containing the variant must be at least
+0.05; change this threshold with \fB\-\-homozyg\-window\-threshold\fR.
+.HP
+\fB\-\-cluster\fR ['cc'] [{group\-avg | old\-tiebreaks}] ['missing'] ['only2']
+.IP
+Cluster samples using a pairwise similarity statistic (normally IBS).
+* The 'cc' modifier forces every cluster to have at least one case and one
+.IP
+control.
+.IP
+* The 'group\-avg' modifier causes clusters to be joined based on average
+.IP
+instead of minimum pairwise similarity.
+.IP
+* The 'missing' modifier causes clustering to be based on
+.IP
+identity\-by\-missingness instead of identity\-by\-state, and writes a
+space\-delimited identity\-by\-missingness matrix to disk.
+.IP
+* The 'only2' modifier causes only a .cluster2 file (which is valid input
+.IP
+for \fB\-\-within\fR) to be written; otherwise 2 other files will be produced.
+.IP
+* By default, IBS ties are not broken in the same manner as PLINK 1.07, so
+.TP
+final cluster solutions tend to differ.
+This is generally harmless.
+.IP
+However, to simplify testing, you can use the 'old\-tiebreaks' modifier to
+force emulation of the old algorithm.
+.HP
+\fB\-\-pca\fR [count] ['header'] ['tabs'] ['var\-wts']
+.IP
+Calculates a variance\-standardized relationship matrix (use
+\fB\-\-make\-rel\fR/\-\-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
+.IP
+approximate linkage equilibrium.
+.IP
+* You can change the number of PCs by passing a numeric parameter.
+* The 'header' modifier adds a header line to the .eigenvec output file.
+.IP
+(For compatibility with the GCTA flag of the same name, the default is no
+header line.)
+.IP
+* The 'tabs' modifier causes the .eigenvec file(s) to be tab\-delimited.
+* The 'var\-wts' modifier requests an additional .eigenvec.var file with PCs
+.IP
+expressed as variant weights instead of sample weights.
+.HP
+\fB\-\-neighbour\fR <n1> <n2>
+.IP
+(alias: \fB\-\-neighbor\fR)
+Report IBS distances from each sample to their n1th\- to n2th\-nearest
+neighbors, associated Z\-scores, and the identities of those neighbors.
+Useful for outlier detection.
+.HP
+\fB\-\-assoc\fR ['perm' | 'mperm='<value>] ['perm\-count'] [{fisher | fisher\-midp}]
+.IP
+['counts'] ['set\-test']
+.HP
+\fB\-\-assoc\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['qt\-means'] ['lin']
+.IP
+['set\-test']
+.HP
+\fB\-\-model\fR ['perm' | 'mperm='<value>] ['perm\-count']
+.IP
+[{fisher | fisher\-midp | trend\-only}] ['set\-test']
+[{dom | rec | gen | trend}]
+.IP
+Basic association analysis report.
+Given a case/control phenotype, \fB\-\-assoc\fR performs a 1df chi\-square allelic
+test, while \fB\-\-model\fR performs 4 other tests as well (1df dominant gene
+action, 1df recessive gene action, 2df genotypic, Cochran\-Armitage trend).
+* With 'fisher'/'fisher\-midp', Fisher's exact test is used to generate
+.TP
+p\-values.
+\&'fisher\-midp' also applies Lancaster's mid\-p adjustment.
+.IP
+* 'perm' causes an adaptive permutation test to be performed.
+* 'mperm='<value> causes a max(T) permutation test with the specified
+.IP
+number of replications to be performed.
+.IP
+* 'perm\-count' causes the permutation test report to include counts instead
+.IP
+of frequencies.
+.IP
+* 'counts' causes \fB\-\-assoc\fR to report allele counts instead of frequencies.
+* 'set\-test' tests the significance of variant sets. Requires permutation;
+.IP
+can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max.
+.IP
+* 'dom', 'rec', 'gen', and 'trend' force the corresponding test to be used
+.TP
+as the basis for \fB\-\-model\fR permutation.
+(By default, the most significant
+.IP
+result among the allelic, dominant, and recessive tests is used.)
+.IP
+* 'trend\-only' causes only the trend test to be performed.
+Given a quantitative phenotype, \fB\-\-assoc\fR normally performs a Wald test.
+* In this case, the 'qt\-means' modifier causes trait means and standard
+.IP
+deviations stratified by genotype to be reported as well.
+.IP
+* 'lin' causes the Lin statistic to be computed, and makes it the basis for
+.IP
+multiple\-testing corrections and permutation tests.
+.IP
+Several other flags (most notably, \fB\-\-aperm\fR) can be used to customize the
+permutation test.
+.HP
+\fB\-\-mh\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['set\-test']
+.IP
+(alias: \fB\-\-cmh\fR)
+.HP
+\fB\-\-bd\fR ['perm' | 'perm\-bd' | 'mperm='<value>] ['perm\-count'] ['set\-test']
+.HP
+\fB\-\-mh2\fR
+.HP
+\fB\-\-homog\fR
+.IP
+Given a case/control phenotype and a set of clusters, \fB\-\-mh\fR computes 2x2xK
+Cochran\-Mantel\-Haenszel statistics for each variant, while \fB\-\-bd\fR also
+performs the Breslow\-Day test for odds ratio homogeneity. Permutation and
+variant set testing based on the CMH (default) or Breslow\-Day (when
+\&'perm\-bd' is present) statistic are supported.
+The following similar analyses are also available:
+* \fB\-\-mh2\fR swaps the roles of case/control status and cluster membership,
+.IP
+performing a phenotype\-stratified IxJxK Cochran\-Mantel\-Haenszel test on
+association between cluster assignments and genotypes.
+.IP
+* \fB\-\-homog\fR executes an alternative to the Breslow\-Day test, based on
+.IP
+partitioning of the chi\-square statistic.
+.HP
+\fB\-\-gxe\fR [covariate index]
+.IP
+Given both a quantitative phenotype and a case/control covariate loaded
+with \fB\-\-covar\fR defining two groups, \fB\-\-gxe\fR compares the regression coefficient
+derived from considering only members of one group to the regression
+coefficient derived from considering only members of the other. By
+default, the first covariate in the \fB\-\-covar\fR file defines the groups; use
+e.g. "\-\-gxe 3" to base them on the third covariate instead.
+.HP
+\fB\-\-linear\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['set\-test']
+.IP
+[{genotypic | hethom | dominant | recessive | no\-snp}]
+['hide\-covar'] [{sex | no\-x\-sex}] ['interaction'] ['beta']
+['standard\-beta'] ['intercept']
+.HP
+\fB\-\-logistic\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['set\-test']
+.IP
+[{genotypic | hethom | dominant | recessive | no\-snp}]
+['hide\-covar'] [{sex | no\-x\-sex}] ['interaction'] ['beta']
+['intercept']
+.IP
+Multi\-covariate association analysis on a quantitative (\fB\-\-linear\fR) or
+case/control (\fB\-\-logistic\fR) phenotype. Normally used with \fB\-\-covar\fR.
+* 'perm' normally causes an adaptive permutation test to be performed on
+.IP
+the main effect, while 'mperm='<value> starts a max(T) permutation test.
+.IP
+* 'perm\-count' causes the permutation test report to include counts instead
+.IP
+of frequencies.
+.TP
+* 'set\-test' tests the significance of variant sets.
+Requires permutation;
+.IP
+can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max.
+.IP
+* The 'genotypic' modifier adds an additive effect/dominance deviation 2df
+.IP
+joint test (0/1/2 and 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0
+coding instead. If permutation is also requested, these modifiers cause
+permutation to be based on the joint test.
+.IP
+* 'dominant' and 'recessive' specify a model assuming full dominance or
+.IP
+recessiveness, respectively, for the A1 allele.
+.IP
+* 'no\-snp' causes regression to be performed only on the phenotype and the
+.TP
+covariates, without reference to genomic data.
+If permutation is also
+.IP
+requested, results are reported for all covariates.
+.IP
+* 'hide\-covar' removes covariate\-specific lines from the report.
+* By default, sex (male = 1, female = 0) is automatically added as a
+.TP
+covariate on X chromosome variants, and nowhere else.
+The 'sex' modifier
+.IP
+causes it to be added everywhere, while 'no\-x\-sex' excludes it.
+.TP
+* 'interaction' adds genotype x covariate interactions to the model.
+This
+.IP
+cannot be used with the usual permutation tests; use \fB\-\-tests\fR to define
+the permutation test statistic instead.
+.IP
+* 'intercept' causes intercepts to be included in the main report.
+* For logistic regressions, the 'beta' modifier causes regression
+.IP
+coefficients instead of odds ratios to be reported.
+.IP
+* With \fB\-\-linear\fR, the 'standard\-beta' modifier standardizes the phenotype
+.IP
+and all predictors to zero mean and unit variance before regression.
+.HP
+\fB\-\-dosage\fR <allele dosage file> ['noheader'] ['skip0='<i>] ['skip1='<j>]
+.IP
+['skip2='<k>] ['dose1'] ['format='<m>] ['Zout']
+[{occur | standard\-beta}] ['sex'] ['case\-control\-freqs']
+.HP
+\fB\-\-dosage\fR <list file> list [{sepheader | noheader}] ['skip0='<i>]
+.IP
+['skip1='<j>] ['skip2='<k>] ['dose1'] ['format='<m>] ['Zout']
+[{occur | standard\-beta}] ['sex'] ['case\-control\-freqs']
+.HP
+\fB\-\-write\-dosage\fR
+.IP
+Process (possibly gzipped) text files with variant\-major allelic dosage
+data. This cannot be used with a regular input fileset; instead, you must
+*only* specify a .fam and possibly a .map file, and you can't specify any
+other commands.
+* PLINK 2.0 will have first\-class support for genotype probabilities. An
+.IP
+equivalent data import flag will be provided then, and \fB\-\-dosage\fR will be
+retired.
+.IP
+* By default, \fB\-\-dosage\fR assumes that only one allelic dosage file should be
+.TP
+loaded.
+To specify multiple files,
+.TP
+1. create a master list with one entry per line.
+There are normally two
+.IP
+supported formats for this list: just a filename per line, or variant
+batch numbers in the first column and filenames in the second.
+.IP
+2. Provide the name of that list as the first \fB\-\-dosage\fR parameter..
+3. Add the 'list' modifier.
+.IP
+* By default, \fB\-\-dosage\fR assumes the allelic dosage file(s) contain a header
+.IP
+line, which has 'SNP' in column i+1, 'A1' in column i+j+2, 'A2' in column
+i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are
+normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
+respectively.) If such a header line is not present,
+* when all samples appear in the same order as they do in the .fam file,
+.IP
+you can use the 'noheader' modifier.
+.IP
+* Otherwise, use the 'sepheader' modifier, and append sample ID filenames
+.IP
+to your 'list' file entries.
+.IP
+* The 'format=' modifier lets you specify the number of values used to
+.TP
+represent each dosage.
+\&'format=1' normally indicates a single 0..2 A1
+.TP
+expected count; 'dose1' modifies this to a 0..1 frequency.
+\&'format=2'
+.IP
+(the default) indicates a 0..1 homozygous A1 likelihood followed by a
+0..1 het likelihood, while 'format=3' indicates 0..1 hom A1, 0..1 het,
+0..1 hom A2.
+.IP
+* 'Zout' causes the output file to be gzipped.
+* Normally, an association analysis is performed. 'standard\-beta' and
+.IP
+\&'sex' behave as they are supposed to with \fB\-\-linear\fR/\-\-logistic.
+\&'case\-control\-freqs' causes case and control allele frequencies to be
+reported separately.
+.IP
+* There are three alternate modes which cause the association analysis to
+.IP
+be skipped.
+* 'occur' requests a simple variant occurrence report.
+* \fB\-\-write\-dosage\fR causes a simple merged file matching the 'format'
+.IP
+specification (not including 'dose1') to be generated.
+.IP
+* \fB\-\-score\fR applies a linear scoring system to the dosages.
+.HP
+\fB\-\-lasso\fR <h2 estimate> [min lambda] ['report\-zeroes']
+.TP
+Estimate variant effect sizes via LASSO regression.
+You must provide an
+.IP
+additive heritability estimate to calibrate the regression.
+Note that this method may require a very large sample size (e.g. hundreds
+of thousands) to be effective on complex polygenic traits.
+.HP
+\fB\-\-test\-missing\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['midp']
+.IP
+Check for association between missingness and case/control status, using
+Fisher's exact test. (Het. haploids are treated as missing.)
+The 'midp' modifier causes Lancaster's mid\-p adjustment to be applied.
+.HP
+\fB\-\-make\-perm\-pheno\fR <ct>
+.IP
+Generate phenotype permutations and write them to disk, without invoking an
+association test.
+.HP
+\fB\-\-tdt\fR [{exact | exact\-midp | poo}] ['perm' | 'mperm='<value>] ['perm\-count']
+.IP
+[{parentdt1 | parentdt2 | pat | mat}] ['set\-test']
+.IP
+Report transmission disequilibrium test statistics, given case/control
+phenotypes and pedigree information.
+* A Mendel error check is performed before the main tests; offending
+.IP
+genotypes are treated as missing by this analysis.
+.IP
+* By default, the basic TDT p\-value is based on a chi\-square test unless
+.IP
+you request the exact binomial test with 'exact' or 'exact\-midp'.
+.IP
+* 'perm'/'mperm=' requests a family\-based adaptive or max(T) permutation
+.TP
+test.
+By default, the permutation test statistic is the basic TDT
+.IP
+p\-value; 'parentdt1'/'parentdt2' cause parenTDT or combined test
+p\-values, respectively, to be considered instead.
+.TP
+* 'set\-test' tests the significance of variant sets.
+This cannot be used
+.IP
+with exact tests for now.
+.IP
+The 'poo' modifier causes a parent\-of\-origin analysis to be performed
+instead, with transmissions from heterozygous fathers and heterozygous
+mothers considered separately.
+* The parent\-of\-origin analysis does not currently support exact tests..
+* By default, the permutation test statistic is the absolute
+.IP
+parent\-of\-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT
+chi\-square statistics, respectively, to be considered instead.
+.HP
+\fB\-\-qfam\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['emp\-se']
+.HP
+\fB\-\-qfam\-parents\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['emp\-se']
+.HP
+\fB\-\-qfam\-between\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['emp\-se']
+.HP
+\fB\-\-qfam\-total\fR ['perm' | 'mperm='<value>] ['perm\-count'] ['emp\-se']
+.IP
+QFAM family\-based association test for quantitative traits.
+* A Mendel error check is performed before the main tests; offending
+.IP
+genotypes are treated as missing by this analysis.
+.TP
+* This procedure requires permutation.
+\&'perm' and 'perm\-count' have the
+.TP
+usual meanings.
+However, 'mperm='<value> just specifies a fixed number
+.IP
+of permutations; the method does not support a proper max(T) test.
+.IP
+* The 'emp\-se' modifier adds BETA and EMP_SE (empirical standard error for
+.IP
+beta) fields to the .perm output file.
+.HP
+\fB\-\-annotate\fR <PLINK report> ['attrib='<file>] ['ranges='<file>]
+.IP
+['filter='<file>] ['snps='<file>] [{NA | prune}] ['block']
+['subset='<file>] ['minimal'] ['distance']
+.TP
+Add annotations to a variant\-based PLINK report.
+This requires an
+.IP
+annotation source:
+* 'attrib='<file> specifies a (possibly gzipped) attribute file.
+* 'ranges='<file> specifies a gene/range list file.
+(Both source types can be specified simultaneously.) The following options
+are also supported:
+* 'filter='<file> causes only variants within one of the ranges in the file
+.IP
+to be included in the new report.
+.IP
+* 'snps='<file> causes only variants named in the file to be included in
+.IP
+the new report.
+.IP
+* The 'NA' modifier causes unannotated variants to have 'NA' instead of '.'
+.IP
+in the new report's ANNOT column, while the 'prune' modifier excludes
+them entirely.
+.IP
+* The 'block' modifier replaces the single ANNOT column with a 0/1\-coded
+.IP
+column for each possible annotation.
+.IP
+* With 'ranges',
+.IP
+* 'subset='<file> causes only intervals named in the subset file to be
+.IP
+loaded from the ranges file.
+.IP
+* interval annotations normally come with a parenthesized signed distance
+.IP
+to the interval boundary (0 if the variant is located inside the
+interval; this is always true without \fB\-\-border\fR). They can be excluded
+with the 'minimal' modifier.
+.IP
+* the 'distance' modifier adds 'DIST' and 'SGN' columns describing signed
+.IP
+distance to the nearest interval.
+.IP
+* When \fB\-\-pfilter\fR is present, high p\-values are filtered out.
+.HP
+\fB\-\-clump\fR <PLINK report filename(s)...>
+.IP
+Process association analysis report(s) with 'SNP' and p\-value columns,
+organizing results by LD\-based clumps. Multiple filenames can be separated
+by spaces or commas.
+.HP
+\fB\-\-gene\-report\fR <PLINK report> <gene range file>
+.IP
+Generate a gene\-based report from a variant\-based report.
+* When \fB\-\-pfilter\fR is present, high p\-values are filtered out.
+* When \fB\-\-extract\fR (without 'range') is present, only variants named in the
+.HP
+\fB\-\-extract\fR file are considered.
+.HP
+\fB\-\-meta\-analysis\fR <PLINK report filenames...>
+.HP
+\fB\-\-meta\-analysis\fR <PLINK report filenames...> + [{logscale | qt}]
+.IP
+[{no\-map | no\-allele}] ['study'] ['report\-all']
+['weighted\-z']
+.IP
+Perform a meta\-analysis on several variant\-based reports with 'SNP' and
+\&'SE' fields.
+* Normally, an 'OR' odds ratio field must also be present in each input
+.TP
+file.
+With 'logscale', 'BETA' log\-odds values/regression coefficients
+.IP
+are expected instead, but the generated report will still contain odds
+ratio estimates. With 'qt', both input and output values are regression
+betas.
+.TP
+* 'CHR', 'BP', and 'A1' fields are also normally required.
+\&'no\-map' causes
+.IP
+them to all be ignored, while 'no\-allele' causes just 'A1' to be ignored.
+.IP
+* If 'A2' fields are present, and neither 'no\-map' nor 'no\-allele' was
+.TP
+specified, A1/A2 allele flips are handled properly.
+Otherwise, A1
+.IP
+mismatches are thrown out.
+.IP
+* 'study' causes study\-specific effect estimates to be collated in the
+.IP
+meta\-analysis report.
+.IP
+* 'report\-all' causes variants present in only a single input file to be
+.IP
+included in the meta\-analysis report.
+.IP
+* 'weighted\-z' requests weighted Z\-score\-based p\-values (as computed by the
+.IP
+Abecasis Lab's METAL software) in addition to the usual inverse
+variance\-based analysis. This requires P and effective sample size
+fields.
+.IP
+* When \fB\-\-extract\fR (without 'range') is present, only variants named in the
+.HP
+\fB\-\-extract\fR file are considered.
+.IP
+* Unless 'no\-map' is specified, chromosome filters are also respected.
+.HP
+\fB\-\-fast\-epistasis\fR [{boost | joint\-effects | no\-ueki}] ['case\-only']
+.IP
+[{set\-by\-set | set\-by\-all}] ['nop']
+.HP
+\fB\-\-epistasis\fR [{set\-by\-set | set\-by\-all}]
+.TP
+Scan for epistatic interactions.
+\fB\-\-fast\-epistasis\fR inspects 3x3 joint
+.IP
+genotype count tables and only applies to case/control phenotypes, while
+\fB\-\-epistasis\fR performs linear or logistic regression.
+* By default, \fB\-\-fast\-epistasis\fR uses the PLINK 1.07 allele\-based test. Two
+.IP
+newer tests are now supported: 'boost' invokes the likelihood ratio test
+introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting
+Gene\-Gene Interactions in Genome\-wide Case\-Control Studies, while
+\&'joint\-effects' applies the joint effects test introduced in Ueki M,
+Cordell HJ (2012) Improved statistics for genome\-wide interaction
+analysis.
+.IP
+* The original \fB\-\-fast\-epistasis\fR test normally applies the variance and
+.TP
+empty cell corrections suggested by Ueki and Cordell's paper.
+To disable
+.IP
+them, use the 'no\-ueki' modifier.
+.IP
+* 'case\-only' requests a case\-only instead of a case/control test.
+* By default, all pairs of variants across the entire genome are tested.
+.IP
+To just test pairs of variants within a single set, add the 'set\-by\-set'
+modifier and load exactly one set with \fB\-\-set\fR/\-\-make\-set; with exactly two
+sets loaded, all variants in one set are tested against all variants in
+the other. 'set\-by\-all' tests all variants in one set against the entire
+genome instead.
+.IP
+* 'nop' strips p\-values from the main report.
+* These computations can be subdivided with \fB\-\-parallel\fR; however...
+.HP
+\fB\-\-epistasis\-summary\-merge\fR <common file prefix> <ct>
+.IP
+When a \fB\-\-[fast\-]epistasis\fR job is subdivided with \fB\-\-parallel\fR, the main
+report can be assembled at the end by applying Unix 'cat' in the usual
+manner, but the .summary.1, .summary.2, ... files may require a specialized
+merge. \fB\-\-epistasis\-summary\-merge\fR takes care of the latter.
+.HP
+\fB\-\-twolocus\fR <variant ID> <variant ID>
+.IP
+Two\-locus joint genotype count report.
+.HP
+\fB\-\-score\fR <filename> [i] [j] [k] ['header'] [{sum | no\-sum}]
+.IP
+[{no\-mean\-imputation | center}] ['include\-cnt'] ['double\-dosage']
+.IP
+Apply a linear scoring system to each sample.
+The input file should have one line per scored variant. Variant IDs are
+read from column #i, allele codes are read from column #j, and scores are
+read from column #k, where i defaults to 1, j defaults to i+1, and k
+defaults to j+1.
+* The 'header' modifier causes the first nonempty line of the input file to
+.IP
+be ignored; otherwise, \fB\-\-score\fR assumes there is no header line.
+.IP
+* By default, final scores are averages of the valid per\-variant scores..
+.TP
+The 'sum' modifier causes sums to be reported instead.
+(This cannot be
+.TP
+used with 'no\-mean\-imputation'.
+And for backward compatibility, 'sum' is
+.IP
+automatically on with dosage data unless 'no\-sum' is specified.)
+.IP
+* By default, copies of the unnamed allele contribute zero to score, while
+.IP
+missing genotypes contribute an amount proportional to the loaded (via
+\fB\-\-read\-freq\fR) or imputed allele frequency. To throw out missing
+observations instead (decreasing the denominator in the final average
+when this happens), use the 'no\-mean\-imputation' modifier.
+.IP
+* Alternatively, you can use the 'center' modifier to shift all scores to
+.IP
+mean zero.
+.TP
+* This command can be used with dosage data.
+By default, the 'CNT' column
+.IP
+is omitted from the output file in this case; use 'include\-cnt' to keep
+it. Also, note that scores are multiplied by 0..1 dosages, not 0..2
+diploid allele counts, unless the 'double\-dosage' modifier is present.
+.HP
+\fB\-\-R\fR <R script file> ['debug']
+.IP
+Connect to a Rserve (preferably version 1.7 or later) background process,
+and execute the Rplink function defined in the input file. (Unless the
+\&'debug' modifier is present; in that case, the R commands that PLINK would
+have tried to execute are logged to a file.)
+.HP
+\fB\-\-write\-var\-ranges\fR <block ct>
+.TP
+Divide the set of variants into equal\-size blocks.
+(Can be used with
+.HP
+\fB\-\-snps\fR to split a job across multiple machines.)
+.PP
+The following other flags are supported. (Order of operations is described at
+https://www.cog\-genomics.org/plink/1.9/order .)
+.HP
+\fB\-\-script\fR <fname> : Include command\-line options from file.
+.TP
+\fB\-\-rerun\fR [log]
+: Rerun commands in log (default 'plink.log').
+.TP
+\fB\-\-version\fR
+: Display only version number before exiting.
+.TP
+\fB\-\-silent\fR
+: Suppress output to console.
+.TP
+\fB\-\-gplink\fR
+: Reserved for interoperation with gPLINK.
+.HP
+\fB\-\-missing\-genotype\fR <char> : Set missing genotype code (normally '0').
+.TP
+\fB\-\-double\-id\fR
+: Set both FIDs and IIDs to the VCF/BCF sample ID.
+.TP
+\fB\-\-const\-fid\fR [ID]
+: Set all FIDs to the given constant (default '0').
+.TP
+\fB\-\-id\-delim\fR [d]
+: Parse sample IDs as <FID><d><IID> (default delim '_').
+.HP
+\fB\-\-vcf\-idspace\-to\fR <c> : Convert spaces in sample IDs to the given character.
+.HP
+\fB\-\-biallelic\-only\fR ['strict'] ['list'] : Skip VCF variants with 2+ ALT alleles.
+.TP
+\fB\-\-vcf\-min\-qual\fR <val>
+: Skip VCF variants with low/missing QUAL.
+.HP
+\fB\-\-vcf\-filter\fR [exception(s)...] : Skip variants which have FILTER failures.
+.TP
+\fB\-\-vcf\-require\-gt\fR
+: Skip variants with no GT field.
+.TP
+\fB\-\-vcf\-min\-gq\fR <val>
+: No\-call a genotype when GQ is below the
+given threshold.
+.TP
+\fB\-\-vcf\-min\-gp\fR <val>
+: No\-call a genotype when 0\-1 scaled GP is
+below the given threshold.
+.TP
+\fB\-\-vcf\-half\-call\fR <m>
+: Specify how '0/.' and similar VCF GT values should be
+handled. The following four modes are supported:
+* 'error'/'e' (default) errors out and reports line #.
+* 'haploid'/'h' treats them as haploid calls.
+* 'missing'/'m' treats them as missing.
+* 'reference'/'r' treats the missing value as 0.
+.TP
+\fB\-\-oxford\-single\-chr\fR <chr nm> : Specify single\-chromosome .gen file with
+ignorable first column.
+.HP
+\fB\-\-oxford\-pheno\-name\fR <col nm> : Import named phenotype from the .sample file.
+.TP
+\fB\-\-hard\-call\-threshold\fR <val>
+: When an Oxford\-format fileset is loaded, calls
+.TP
+\fB\-\-hard\-call\-threshold\fR random
+with uncertainty level greater than 0.1 are
+normally treated as missing. You can adjust
+this threshold by providing a numeric
+parameter, or randomize all calls with
+\&'random'.
+.HP
+\fB\-\-missing\-code\fR [string list] : Comma\-delimited list of missing phenotype
+.TP
+(alias: \fB\-\-missing_code\fR)
+values for Oxford\-format filesets (def. 'NA').
+.TP
+\fB\-\-simulate\-ncases\fR <num>
+: Set \fB\-\-simulate\fR case count (default 1000).
+.TP
+\fB\-\-simulate\-ncontrols\fR <n>
+: Set \fB\-\-simulate\fR control count (default 1000).
+.HP
+\fB\-\-simulate\-prevalence\fR <p> : Set \fB\-\-simulate\fR disease prevalence (default 0.01).
+.TP
+\fB\-\-simulate\-n\fR <num>
+: Set \fB\-\-simulate\-qt\fR sample count (default 1000).
+.HP
+\fB\-\-simulate\-label\fR <prefix> : Set \fB\-\-simulate[\-qt]\fR FID/IID name prefix.
+.HP
+\fB\-\-simulate\-missing\fR <freq> : Set \fB\-\-simulate[\-qt]\fR missing genotype frequency.
+.TP
+\fB\-\-allow\-extra\-chr\fR ['0']
+: Permit unrecognized chromosome codes. The '0'
+.TP
+(alias: \fB\-\-aec\fR)
+modifier causes them to be treated as if they had
+been set to zero.
+.HP
+\fB\-\-chr\-set\fR <autosome ct> ['no\-x'] ['no\-y'] ['no\-xy'] ['no\-mt'] :
+.TP
+Specify a nonhuman chromosome set.
+The first parameter sets the number of
+.IP
+diploid autosome pairs if positive, or haploid chromosomes if negative.
+Given diploid autosomes, the remaining modifiers indicate the absence of
+the named non\-autosomal chromosomes.
+.HP
+\fB\-\-cow\fR/\-\-dog/\-\-horse/\-\-mouse/\-\-rice/\-\-sheep : Shortcuts for those species.
+.TP
+\fB\-\-autosome\-num\fR <value>
+: Alias for "\-\-chr\-set <value> no\-y no\-xy no\-mt".
+.TP
+\fB\-\-cm\-map\fR <fname pattern> [chr] : Use SHAPEIT\-format recombination maps to set
+centimorgan positions. To process more than
+one chromosome, include a '@' in the first
+parameter where the chrom. number belongs,
+e.g. 'genetic_map_chr at _combined_b37.txt'.
+.TP
+\fB\-\-zero\-cms\fR
+: Zero out centimorgan positions.
+.HP
+\fB\-\-allow\-no\-samples\fR : Allow the input fileset to contain no samples.
+.TP
+\fB\-\-allow\-no\-vars\fR
+: Allow the input fileset to contain no variants.
+.TP
+\fB\-\-pheno\fR <fname>
+: Load phenotype data from the specified file, instead of
+using the values in the main input fileset.
+.TP
+\fB\-\-all\-pheno\fR
+: For basic association tests, loop through all phenotypes
+in \fB\-\-pheno\fR file.
+.TP
+\fB\-\-mpheno\fR <n>
+: Load phenotype from column (n+2) in \fB\-\-pheno\fR file.
+.TP
+\fB\-\-pheno\-name\fR <c> : If \fB\-\-pheno\fR file has a header row, use column with the
+given name.
+.TP
+\fB\-\-pheno\-merge\fR
+: When the main input fileset contains an phenotype value
+for a sample, but the \fB\-\-pheno\fR file does not, use the
+original value instead of treating the phenotype as
+missing.
+.HP
+\fB\-\-missing\-phenotype\fR <v> : Set missing phenotype value (normally \fB\-9\fR).
+.TP
+\fB\-\-1\fR
+: Expect case/control phenotypes to be coded as
+0 = control, 1 = case, instead of the usual
+0 = missing, 1 = control, 2 = case. This also
+forces phenotypes to be interpreted as case/ctrl.
+.TP
+\fB\-\-make\-pheno\fR <fn> <val> : Define a new case/control phenotype.
+If the val
+parameter is '*', all samples listed in the given
+file are cases, and everyone else is a control.
+(Note that, in some shells, it is necessary to
+surround the * with quotes.)
+Otherwise, all samples with third column entry
+equal to the val parameter are cases, and all other
+samples mentioned in the file are controls.
+.TP
+\fB\-\-tail\-pheno\fR <Lt> [Hbt] : Downcode a scalar phenotype to a case/control
+phenotype. All samples with phenotype values
+greater than Hbt are cases, and all with values
+less than or equal to Lt are controls. If Hbt is
+unspecified, it is equal to Lt; otherwise,
+in\-between phenotype values are set to missing.
+.HP
+\fB\-\-covar\fR <filename> ['keep\-pheno\-on\-missing\-cov'] : Specify covariate file.
+.TP
+\fB\-\-covar\-name\fR <...>
+: Specify covariate(s) in \fB\-\-covar\fR file by name.
+Separate multiple names with spaces or commas, and
+use dashes to designate ranges.
+.TP
+\fB\-\-covar\-number\fR <...>
+: Specify covariate(s) in \fB\-\-covar\fR file by index.
+.TP
+\fB\-\-no\-const\-covar\fR
+: Exclude constant covariates.
+.TP
+\fB\-\-allow\-no\-covars\fR
+: Allow no covariates to be loaded from \fB\-\-covar\fR
+file.
+.HP
+\fB\-\-within\fR <f> ['keep\-NA'] : Specify initial cluster assignments.
+.TP
+\fB\-\-mwithin\fR <n>
+: Load cluster assignments from column n+2.
+.TP
+\fB\-\-family\fR
+: Create a cluster for each family ID.
+.TP
+\fB\-\-loop\-assoc\fR <f> ['keep\-NA']
+: Run specified case/control association
+commands once for each cluster in the file,
+using cluster membership as the phenotype.
+.TP
+\fB\-\-set\fR <filename>
+: Load sets from a .set file.
+.TP
+\fB\-\-set\-names\fR <name(s)...>
+: Load only sets named on the command line.
+Use spaces to separate multiple names.
+.TP
+\fB\-\-subset\fR <filename>
+: Load only sets named in the given text file.
+.HP
+\fB\-\-set\-collapse\-all\fR <set name> : Merge all sets.
+.TP
+\fB\-\-complement\-sets\fR
+: Invert all sets. (Names gain 'C_' prefixes.)
+.HP
+\fB\-\-make\-set\-complement\-all\fR <s> : \fB\-\-set\-collapse\-all\fR + inversion.
+.TP
+\fB\-\-make\-set\fR <filename>
+: Define sets from a list of named bp ranges.
+.TP
+\fB\-\-make\-set\-border\fR <kbs>
+: Stretch regions in \fB\-\-make\-set\fR file.
+.TP
+\fB\-\-make\-set\-collapse\-group\fR
+: Define sets from groups instead of sets in
+\fB\-\-make\-set\fR file.
+.TP
+\fB\-\-keep\fR <filename>
+: Exclude all samples not named in the file.
+.TP
+\fB\-\-remove\fR <filename>
+: Exclude all samples named in the file.
+.TP
+\fB\-\-keep\-fam\fR <filename>
+: Exclude all families not named in the file.
+.HP
+\fB\-\-remove\-fam\fR <filename> : Exclude all families named in the file.
+.HP
+\fB\-\-extract\fR ['range'] <f> : Exclude all variants not named in the file.
+.HP
+\fB\-\-exclude\fR ['range'] <f> : Exclude all variants named in the file..
+.TP
+\fB\-\-keep\-clusters\fR <filename>
+: These can be used individually or in
+.TP
+\fB\-\-keep\-cluster\-names\fR <name(s)...>
+combination to define a list of
+clusters to keep; all samples not in a
+cluster in that list are then excluded.
+Use spaces to separate cluster names
+for \fB\-\-keep\-cluster\-names\fR.
+.TP
+\fB\-\-remove\-clusters\fR <filename>
+: Exclude all clusters named in the file.
+.HP
+\fB\-\-remove\-cluster\-names\fR <name(s)...> : Exclude the named clusters.
+.TP
+\fB\-\-gene\fR <sets...> : Exclude variants not in a set named on the command line.
+(Separate multiple set names with spaces.)
+.TP
+\fB\-\-gene\-all\fR
+: Exclude variants which aren't a member of any set. (PLINK
+1.07 automatically did this under some circumstances.)
+.HP
+\fB\-\-attrib\fR <f> [att lst] : Given a file assigning attributes to variants, and a
+.TP
+\fB\-\-attrib\-indiv\fR <f> [a]
+comma\-delimited list (with no whitespace) of
+attribute names, remove variants/samples which are
+either missing from the file or don't have any of
+the listed attributes. If some attribute names in
+the list are preceded by '\-', they are treated as
+"negative match conditions" instead: variants with
+at least one negative match attribute are removed.
+The first character in the list cannot be a '\-', due
+to how command\-line parsing works; add a comma in
+front to get around this.
+.TP
+\fB\-\-chr\fR <chrs...>
+: Exclude all variants not on the given chromosome(s).
+Valid choices for humans are 0 (unplaced), 1\-22, X, Y, XY,
+and MT. Separate multiple chromosomes with spaces and/or
+commas, and use a dash (no adjacent spaces permitted) to
+denote a range, e.g. "\-\-chr 1\-4, 22, xy".
+.TP
+\fB\-\-not\-chr\fR <...>
+: Reverse of \fB\-\-chr\fR (exclude variants on listed chromosomes).
+.TP
+\fB\-\-autosome\fR
+: Exclude all non\-autosomal variants.
+.TP
+\fB\-\-autosome\-xy\fR
+: Exclude all non\-autosomal variants, except those with
+chromosome code XY (pseudo\-autosomal region of X).
+.TP
+\fB\-\-snps\-only\fR ['just\-acgt'] : Exclude non\-SNP variants.
+By default, SNP = both
+allele codes are single\-character; 'just\-acgt'
+restricts codes to {A,C,G,T,a,c,g,t,<missing>}.
+.TP
+\fB\-\-from\fR <var ID>
+: Use ID(s) to specify a variant range to load. When used
+.TP
+\fB\-\-to\fR
+<var ID> together, both variants must be on the same chromosome.
+.TP
+\fB\-\-snp\fR
+<var ID> : Specify a single variant to load.
+.HP
+\fB\-\-exclude\-snp\fR <> : Specify a single variant to exclude.
+.TP
+\fB\-\-window\fR
+<kbs> : With \fB\-\-snp\fR or \fB\-\-exclude\-snp\fR, loads/excludes all variants
+within half the specified kb distance of the named one.
+.TP
+\fB\-\-from\-bp\fR <pos>
+: Use physical position(s) to define a variant range to
+.TP
+\fB\-\-to\-bp\fR
+<pos> load. \fB\-\-from\-kb\fR/\-\-to\-kb/\-\-from\-mb/\-\-to\-mb allow decimal
+.TP
+\fB\-\-from\-kb\fR <pos>
+values. You must also specify a single chromosome (using
+.TP
+\fB\-\-to\-kb\fR
+<pos> e.g. \fB\-\-chr\fR) when using these flags.
+.HP
+\fB\-\-from\-mb\fR <pos>
+.TP
+\fB\-\-to\-mb\fR
+<pos>
+.TP
+\fB\-\-snps\fR <var IDs...>
+: Use IDs to specify variant range(s) to load or
+.TP
+\fB\-\-exclude\-snps\fR <...>
+exclude. E.g. "\-\-snps rs1111\-rs2222, rs3333, rs4444".
+.TP
+\fB\-\-thin\fR <p>
+: Randomly remove variants, retaining each with prob. p.
+.HP
+\fB\-\-thin\-count\fR <n> : Randomly remove variants until n of them remain.
+.TP
+\fB\-\-bp\-space\fR <bps> : Remove variants so that each pair is no closer than the
+given bp distance. (Equivalent to VCFtools \fB\-\-thin\fR.)
+.TP
+\fB\-\-thin\-indiv\fR <p>
+: Randomly remove samples, retaining with prob. p.
+.TP
+\fB\-\-thin\-indiv\-count\fR <n>
+: Randomly remove samples until n of them remain.
+.TP
+\fB\-\-filter\fR <f> <val(s)...> : Exclude all samples without a 3rd column entry in
+the given file matching one of the given
+space\-separated value(s).
+.TP
+\fB\-\-mfilter\fR <n>
+: Match against (n+2)th column instead.
+.TP
+\fB\-\-geno\fR [val]
+: Exclude variants with missing call frequencies greater
+than a threshold (default 0.1). (Note that the default
+threshold is only applied if \fB\-\-geno\fR is invoked without a
+parameter; when \fB\-\-geno\fR is not invoked, no per\-variant
+missing call frequency ceiling is enforced at all. Other
+inclusion/exclusion default thresholds work the same way.)
+.TP
+\fB\-\-mind\fR [val]
+: Exclude samples with missing call frequencies greater than
+a threshold (default 0.1).
+.TP
+\fB\-\-oblig\-missing\fR <f1> <f2> : Specify blocks of missing genotype calls for
+\fB\-\-geno\fR/\-\-mind to ignore. The first file should
+have variant IDs in the first column and block
+IDs in the second, while the second file should
+have FIDs in the first column, IIDs in the
+second, and block IDs in the third.
+.TP
+\fB\-\-prune\fR
+: Remove samples with missing phenotypes.
+.TP
+\fB\-\-maf\fR [freq]
+: Exclude variants with minor allele frequency lower than
+a threshold (default 0.01).
+.TP
+\fB\-\-max\-maf\fR <freq>
+: Exclude variants with MAF greater than the threshold.
+.TP
+\fB\-\-mac\fR <ct>
+: Exclude variants with minor allele count lower than the
+.TP
+(alias: \fB\-\-min\-ac\fR)
+given threshold.
+.TP
+\fB\-\-max\-mac\fR <ct>
+: Exclude variants with minor allele count greater than
+.TP
+(alias: \fB\-\-max\-ac\fR)
+the given threshold.
+.TP
+\fB\-\-maf\-succ\fR
+: Rule of succession MAF estimation (used in EIGENSOFT).
+Given j observations of one allele and k >= j observations
+of the other, infer a MAF of (j+1) / (j+k+2), rather than
+the default j / (j+k).
+.TP
+\fB\-\-read\-freq\fR <fn> : Estimate MAFs and heterozygote frequencies from the given
+\fB\-\-freq[x]\fR report, instead of the input fileset.
+.TP
+\fB\-\-hwe\fR <p> ['midp'] ['include\-nonctrl'] : Exclude variants with Hardy\-Weinberg
+equilibrium exact test p\-values
+below a threshold.
+.TP
+\fB\-\-me\fR <t> <v> ['var\-first'] : Filter out trios and variants with Mendel error
+rates exceeding the given thresholds.
+.TP
+\fB\-\-me\-exclude\-one\fR [ratio]
+: Make \fB\-\-me\fR exclude only one sample per trio.
+.TP
+\fB\-\-qual\-scores\fR <f> [qcol] [IDcol] [skip] : Filter out variants with
+out\-of\-range quality scores.
+Default range is now [0, \einfty ).
+.TP
+\fB\-\-qual\-threshold\fR <min qual score>
+: Set \fB\-\-qual\-scores\fR range floor.
+.TP
+\fB\-\-qual\-max\-threshold\fR <max qual score>
+: Set \fB\-\-qual\-scores\fR range ceiling.
+.TP
+\fB\-\-allow\-no\-sex\fR
+: Do not treat ambiguous\-sex samples as having missing
+phenotypes in analysis commands. (Automatic \fI\,/w\/\fP \fB\-\-no\-sex\fR.)
+.TP
+\fB\-\-must\-have\-sex\fR
+: Force ambiguous\-sex phenotypes to missing on
+\fB\-\-make\-bed\fR/\-\-make\-just\-fam/\-\-recode/\-\-write\-covar.
+.TP
+\fB\-\-filter\-cases\fR
+: Include only cases in the current analysis.
+.TP
+\fB\-\-filter\-controls\fR
+: Include only controls.
+.TP
+\fB\-\-filter\-males\fR
+: Include only males.
+.TP
+\fB\-\-filter\-females\fR
+: Include only females.
+.TP
+\fB\-\-filter\-founders\fR
+: Include only founders.
+.HP
+\fB\-\-filter\-nonfounders\fR : Include only nonfounders.
+.TP
+\fB\-\-nonfounders\fR
+: Include nonfounders in allele freq/HWE calculations.
+.HP
+\fB\-\-make\-founders\fR ['require\-2\-missing'] ['first'] :
+.IP
+Clear parental IDs for those with 1+ missing parent(s).
+.TP
+\fB\-\-recode\-allele\fR <fn> : With \fB\-\-recode\fR A/A\-transpose/AD, count alleles named in
+the file (otherwise A1 alleles are always counted).
+.TP
+\fB\-\-output\-chr\fR <MT code> : Set chromosome coding scheme in output files by
+providing the desired human mitochondrial code.
+(Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
+and 'chrMT'.)
+.TP
+\fB\-\-output\-missing\-genotype\fR <ch> : Set the code used to represent missing
+genotypes in output files (normally the
+\fB\-\-missing\-genotype\fR value).
+.TP
+\fB\-\-output\-missing\-phenotype\fR <s> : Set the string used to represent missing
+phenotypes in output files (normally the
+\fB\-\-missing\-phenotype\fR value).
+.TP
+\fB\-\-zero\-cluster\fR <f> : In combination with \fB\-\-within\fR/\-\-family, set blocks of
+genotype calls to missing. The input file should have
+variant IDs in the first column and cluster IDs in the
+second. This must now be used with \fB\-\-make\-bed\fR and no
+other output commands.
+.TP
+\fB\-\-set\-hh\-missing\fR
+: Cause \fB\-\-make\-bed\fR and \fB\-\-recode\fR to set heterozygous
+haploid genotypes to missing.
+.TP
+\fB\-\-set\-mixed\-mt\-missing\fR : Cause \fB\-\-make\-bed\fR and \fB\-\-recode\fR to set mixed MT
+genotypes to missing.
+.HP
+\fB\-\-split\-x\fR <bp1> <bp2> ['no\-fail']
+.HP
+\fB\-\-split\-x\fR <build> ['no\-fail'] :
+.IP
+Changes chromosome code of all chrX variants with bp position <= bp1 or >=
+bp2 to XY. The following build codes are supported as shorthand:
+* 'b36'/'hg18' = NCBI 36, 2709521/154584237
+* 'b37'/'hg19' = GRCh37, 2699520/154931044
+* 'b38'/'hg38' = GRCh38, 2781479/155701383
+By default, PLINK errors out when no variants would be affected by
+\fB\-\-split\-x\fR; the 'no\-fail' modifier (useful in scripts) overrides this.
+.HP
+\fB\-\-merge\-x\fR ['no\-fail'] : Merge XY chromosome back with X.
+.TP
+\fB\-\-set\-me\-missing\fR
+: Cause \fB\-\-make\-bed\fR to set Mendel errors to missing.
+.TP
+\fB\-\-fill\-missing\-a2\fR
+: Cause \fB\-\-make\-bed\fR to replace all missing calls with
+homozygous A2 calls.
+.TP
+\fB\-\-set\-missing\-var\-ids\fR <t>
+: Given a template string with a '@' where the
+chromosome code should go and '#' where the bp
+coordinate belongs, \fB\-\-set\-missing\-var\-ids\fR
+assigns chromosome\-and\-bp\-based IDs to unnamed
+variants.
+You may also use '$1' and '$2' to refer to
+allele names in the template string, and in
+fact this becomes essential when multiple
+variants share the same coordinate.
+.TP
+\fB\-\-new\-id\-max\-allele\-len\fR <n> : Specify maximum number of leading characters
+from allele names to include in new variant IDs
+(default 23).
+.HP
+\fB\-\-missing\-var\-code\fR <string> : Change unnamed variant code (default '.').
+.TP
+\fB\-\-update\-chr\fR
+<f> [chrcol] [IDcol] [skip] : Update variant chromosome codes.
+.TP
+\fB\-\-update\-cm\fR
+<f> [cmcol] [IDcol] [skip] : Update centimorgan positions.
+.TP
+\fB\-\-update\-map\fR
+<f> [bpcol] [IDcol] [skip] : Update variant bp positions.
+.HP
+\fB\-\-update\-name\fR <f> [newcol] [oldcol] [skip] : Update variant IDs..
+.HP
+\fB\-\-update\-alleles\fR <fname> : Update variant allele codes.
+.TP
+\fB\-\-allele1234\fR ['multichar'] : Interpret/recode A/C/G/T alleles as 1/2/3/4.
+With 'multichar', converts all A/C/G/Ts in
+allele names to 1/2/3/4s.
+.HP
+\fB\-\-alleleACGT\fR ['multichar'] : Reverse of \fB\-\-allele1234\fR.
+.TP
+\fB\-\-update\-ids\fR <f>
+: Update sample IDs.
+.HP
+\fB\-\-update\-parents\fR <f> : Update parental IDs.
+.TP
+\fB\-\-update\-sex\fR <f> [n] : Update sexes.
+Sex (1 or M = male, 2 or F = female, 0
+= missing) is loaded from column n+2 (default n is 1).
+.TP
+\fB\-\-flip\fR <filename>
+: Flip alleles (A<\->T, C<\->G) for SNP IDs in the file.
+.TP
+\fB\-\-flip\-subset\fR <fn>
+: Only apply \fB\-\-flip\fR to samples in \fB\-\-flip\-subset\fR file.
+.HP
+\fB\-\-flip\-scan\-window\fR <ct+1> : Set \fB\-\-flip\-scan\fR max variant ct dist. (def. 10).
+.HP
+\fB\-\-flip\-scan\-window\-kb\fR <x> : Set \fB\-\-flip\-scan\fR max kb distance (default 1000).
+.HP
+\fB\-\-flip\-scan\-threshold\fR <x> : Set \fB\-\-flip\-scan\fR min correlation (default 0.5).
+.TP
+\fB\-\-keep\-allele\-order\fR
+: Keep the allele order defined in the .bim file,
+.TP
+\fB\-\-real\-ref\-alleles\fR
+instead of forcing A2 to be the major allele.
+\fB\-\-real\-ref\-alleles\fR also removes 'PR' from the INFO
+values emitted by \fB\-\-recode\fR vcf{,\-fid,\-iid}.
+.HP
+\fB\-\-a1\-allele\fR <f> [a1col] [IDcol] [skip] : Force alleles in the file to A1.
+.HP
+\fB\-\-a2\-allele\fR <filename> [a2col] [IDcol] [skip] :
+.TP
+Force alleles in the file to A2.
+("\-\-a2\-allele <VCF filename> 4 3 '#'",
+.IP
+which scrapes reference allele assignments from a VCF file, is especially
+useful.)
+.TP
+\fB\-\-indiv\-sort\fR <m> [f] : Specify FID/IID sort order.
+The following four modes
+are supported:
+* 'none'/'0' keeps samples in the order they were
+.TP
+loaded.
+Default for non\-merge operations.
+.TP
+* 'natural'/'n' invokes 'natural sort', e.g.
+\&'id2' < 'ID3' < 'id10'. Default when merging.
+.TP
+* 'ascii'/'a' sorts in ASCII order, e.g.
+\&'ID3' < 'id10' < 'id2'.
+.TP
+* 'file'/'f' uses the order in the given file (named
+in the second parameter).
+.TP
+For now, only \fB\-\-merge\fR/\-\-bmerge/\-\-merge\-list and
+\fB\-\-make\-bed\fR/\-\-make\-just\-fam respect this flag.
+.HP
+\fB\-\-with\-phenotype\fR ['no\-parents'] [{no\-sex | female\-2}] :
+.IP
+Include more sample info in new .cov file.
+.TP
+\fB\-\-dummy\-coding\fR [N] ['no\-round'] : Split categorical variables (n categories,
+2 < n <= N, default N is 49) into n\-1
+binary dummy variables when writing
+covariate file.
+.TP
+\fB\-\-merge\-mode\fR <n>
+: Adjust \fB\-\-[b]merge\fR/\-\-merge\-list behavior based on a
+numeric code.
+1 (default) = ignore missing calls, otherwise difference
+.TP
+\-> missing
+2 = only overwrite originally missing calls
+3 = only overwrite when nonmissing in new file
+4/5 = never overwrite and always overwrite, respectively
+6 = report all mismatching calls without merging
+7 = report mismatching nonmissing calls without merging
+.TP
+\fB\-\-merge\-equal\-pos\fR
+: With \fB\-\-merge\fR/\-\-bmerge/\-\-merge\-list, merge variants with
+different names but identical positions. (Exception:
+same\-position chromosome code 0 variants aren't merged.)
+.TP
+\fB\-\-mendel\-duos\fR
+: Make Mendel error checks consider samples with only one
+parent in the dataset.
+.TP
+\fB\-\-mendel\-multigen\fR
+: Make Mendel error checks consider (great\-)grandparental
+genotypes when parental genotype data is missing.
+.HP
+\fB\-\-ld\-window\fR <ct+1> : Set \fB\-\-r\fR/\-\-r2 max variant ct pairwise distance (usu. 10).
+.HP
+\fB\-\-ld\-window\-kb\fR <x> : Set \fB\-\-r\fR/\-\-r2 max kb pairwise distance (usually 1000).
+.HP
+\fB\-\-ld\-window\-cm\fR <x> : Set \fB\-\-r\fR/\-\-r2 max centimorgan pairwise distance.
+.HP
+\fB\-\-ld\-window\-r2\fR <x> : Set threshold for \fB\-\-r2\fR report inclusion (usually 0.2).
+.TP
+\fB\-\-ld\-snp\fR <var ID>
+: Set first variant in all \fB\-\-r\fR/\-\-r2 pairs.
+.HP
+\fB\-\-ld\-snps\fR <vID...> : Restrict first \fB\-\-r\fR/\-\-r2 variant to the given ranges.
+.TP
+\fB\-\-ld\-snp\-list\fR <f>
+: Restrict first \fB\-\-r\fR/\-\-r2 var. to those named in the file.
+.TP
+\fB\-\-list\-all\fR
+: Generate the 'all' mode report when using \fB\-\-show\-tags\fR in
+file mode.
+.TP
+\fB\-\-tag\-kb\fR <kbs>
+: Set \fB\-\-show\-tags\fR max tag kb distance (default 250).
+.TP
+\fB\-\-tag\-r2\fR <val>
+: Set \fB\-\-show\-tags\fR min tag r\-squared (default 0.8)
+.TP
+\fB\-\-tag\-mode2\fR
+: Use two\-column \fB\-\-show\-tags\fR (file mode) I/O format.
+.TP
+\fB\-\-ld\-xchr\fR <code>
+: Set chrX model for \fB\-\-indep[\-pairwise]\fR, \fB\-\-r\fR/\-\-r2,
+\fB\-\-flip\-scan\fR, and \fB\-\-show\-tags\fR.
+1 (default) = males coded 0/1, females 0/1/2 (A1 dosage)
+2 = males coded 0/2
+3 = males coded 0/2, but females given double weighting
+.TP
+\fB\-\-blocks\-max\-kb\fR <kbs>
+: Set \fB\-\-blocks\fR maximum haploblock span (def. 200).
+.TP
+\fB\-\-blocks\-min\-maf\fR <cutoff>
+: Adjust \fB\-\-blocks\fR MAF minimum (default 0.05).
+.TP
+\fB\-\-blocks\-strong\-lowci\fR <x>
+: Set \fB\-\-blocks\fR "strong LD" CI thresholds (defaults
+.TP
+\fB\-\-blocks\-strong\-highci\fR <x>
+0.70 and 0.98).
+.HP
+\fB\-\-blocks\-recomb\-highci\fR <x> : Set 'recombination' CI threshold (default 0.90).
+.TP
+\fB\-\-blocks\-inform\-frac\fR <x>
+: Force haploblock <strong LD pairs>:<total
+informative pairs> ratios to be larger than this
+value (default 0.95).
+.TP
+\fB\-\-distance\-wts\fR exp=<x>
+: When computing genomic distances, assign each
+variant a weight of (2q(1\-q))^{\-x}, where q
+is the loaded or inferred MAF.
+.TP
+\fB\-\-read\-dists\fR <dist file> [id file] : Load a triangular binary distance matrix
+instead of recalculating from scratch.
+.TP
+\fB\-\-ppc\-gap\fR <val>
+: Minimum number of base pairs, in thousands, between
+informative pairs of markers used in \fB\-\-genome\fR PPC test.
+500 if unspecified.
+.TP
+\fB\-\-min\fR <cutoff>
+: Specify minimum PI_HAT for inclusion in \fB\-\-genome\fR report.
+.TP
+\fB\-\-max\fR <cutoff>
+: Specify maximum PI_HAT for inclusion in \fB\-\-genome\fR report.
+.TP
+\fB\-\-homozyg\-match\fR <> : Set minimum concordance across jointly homozygous
+variants for a pairwise allelic match to be declared.
+.TP
+\fB\-\-pool\-size\fR <ct>
+: Set minimum size of pools in "\-\-homozyg group" report.
+.TP
+\fB\-\-read\-genome\fR <fn> : Load \fB\-\-genome\fR report for \fB\-\-cluster\fR/\-\-neighbour, instead
+of recalculating IBS and PPC test p\-values from scratch.
+.TP
+\fB\-\-ppc\fR <p\-val>
+: Specify minimum PPC test p\-value within a cluster.
+.TP
+\fB\-\-mc\fR <max size>
+: Specify maximum cluster size.
+.TP
+\fB\-\-mcc\fR <c1> <c2>
+: Specify maximum case and control counts per cluster.
+.TP
+\fB\-\-K\fR <min count>
+: Specify minimum cluster count.
+.TP
+\fB\-\-ibm\fR <val>
+: Specify minimum identity\-by\-missingness.
+.TP
+\fB\-\-match\fR <f> [mv] : Use covariate values to restrict clustering.
+Without
+\fB\-\-match\-type\fR, two samples can only be in the same cluster
+if all covariates match. The optional second parameter
+specifies a covariate value to treat as missing.
+.TP
+\fB\-\-match\-type\fR <f> : Refine interpretation of \fB\-\-match\fR file.
+The \fB\-\-match\-type\fR
+file is expected to be a single line with as many entries
+as the \fB\-\-match\fR file has covariates; '0' entries specify
+"negative matches" (i.e. samples with equal covariate
+values cannot be in the same cluster), '1' entries specify
+"positive matches" (default), and '\-1' causes the
+corresponding covariate to be ignored.
+.HP
+\fB\-\-qmatch\fR <f> [m] : Force all members of a cluster to have similar
+.TP
+\fB\-\-qt\fR <fname>
+quantitative covariate values. The \fB\-\-qmatch\fR file contains
+the covariate values, while the \fB\-\-qt\fR file is a list of
+nonnegative tolerances (and '\-1's marking covariates to
+skip).
+.HP
+\fB\-\-pca\-cluster\-names\fR <...> : These can be used individually or in combination
+.TP
+\fB\-\-pca\-clusters\fR <fname>
+to define a list of clusters to use in the basic
+\fB\-\-pca\fR computation. (\fB\-\-pca\-cluster\-names\fR expects
+a space\-delimited sequence of cluster names,
+while \fB\-\-pca\-clusters\fR expects a file with one
+cluster name per line.) All samples outside
+those clusters will then be projected on to the
+calculated PCs.
+.HP
+\fB\-\-mds\-plot\fR <dims> ['by\-cluster'] ['eigendecomp'] ['eigvals'] :
+.TP
+Multidimensional scaling analysis.
+Requires \fB\-\-cluster\fR.
+.TP
+\fB\-\-cell\fR <thresh>
+: Skip some \fB\-\-model\fR tests when a contingency table entry is
+smaller than the given threshold.
+.TP
+\fB\-\-condition\fR <var ID> [{dominant | recessive}] : Add one variant as a \fB\-\-linear\fR
+or \fB\-\-logistic\fR covariate.
+.TP
+\fB\-\-condition\-list\fR <f> [{dominant | recessive}] : Add variants named in the
+file as \fB\-\-linear\fR/\-\-logistic
+covariates.
+.TP
+\fB\-\-parameters\fR <...>
+: Include only the given covariates/interactions in the
+\fB\-\-linear\fR/\-\-logistic models, identified by a list of
+1\-based indices and/or ranges of them.
+.TP
+\fB\-\-tests\fR <all> [...] : Perform a (joint) test on the specified term(s) in the
+\fB\-\-linear\fR/\-\-logistic model, identified by 1\-based
+indices and/or ranges of them. If permutation was
+requested, it is based on this test.
+* Note that, when \fB\-\-parameters\fR is also present, the
+.TP
+indices refer to the terms remaining AFTER pruning by
+\fB\-\-parameters\fR.
+.IP
+* You can use "\-\-tests all" to include all terms.
+.TP
+\fB\-\-vif\fR <max VIF>
+: Set VIF threshold for \fB\-\-linear\fR multicollinearity check
+(default 50).
+.TP
+\fB\-\-xchr\-model\fR <code> : Set the X chromosome \fB\-\-linear\fR/\-\-logistic model.
+0 = skip sex and haploid chromosomes
+1 (default) = add sex as a covariate on X chromosome
+2 = code male genotypes 0/2 instead of 0/1
+3 = test for interaction between genotype and sex
+.TP
+\fB\-\-lasso\-select\-covars\fR [cov(s)...] : Subject some or all covariates to LASSO
+model selection.
+.TP
+\fB\-\-adjust\fR ['gc'] ['log10'] ['qq\-plot'] : Report some multiple\-testing
+corrections.
+.TP
+\fB\-\-lambda\fR <val>
+: Set genomic control lambda for \fB\-\-adjust\fR.
+.TP
+\fB\-\-ci\fR <size>
+: Report confidence intervals for odds ratios.
+.TP
+\fB\-\-pfilter\fR <val>
+: Filter out association test results with higher p\-values.
+.HP
+\fB\-\-aperm\fR <min perms \- 1> [max perms] [alpha] [beta] [init interval] [slope] :
+.IP
+Set up to six parameters controlling adaptive permutation tests.
+* The first two control the minimum and maximum number of permutations that
+.IP
+may be run for each variant; default values are 5 and 1000000.
+.TP
+* The next two control the early termination condition.
+A
+.IP
+100% * (1 \- beta/2T) confidence interval is calculated for each empirical
+p\-value, where T is the total number of variants; whenever this
+confidence interval doesn't contain alpha, the variant is exempted from
+further permutation testing. Default values are 0 and 1e\-4.
+.TP
+* The last two control when the early termination condition is checked.
+If
+.IP
+a check occurs at permutation #p, the next check occurs after
+<slope>p + <init interval> more permutations (rounded down). Default
+initial interval is 1, and default slope is 0.001.
+.TP
+\fB\-\-mperm\-save\fR
+: Save best max(T) permutation test statistics.
+.HP
+\fB\-\-mperm\-save\-all\fR : Save all max(T) permutation test statistics..
+.TP
+\fB\-\-set\-p\fR <p\-val>
+: Adjust set test significant variant p\-value ceiling
+(default 0.05).
+.TP
+\fB\-\-set\-r2\fR [v] ['write'] : Adjust set test significant variant pairwise r^2
+ceiling (default 0.5). 'write' causes violating
+.IP
+pairs to be dumped to <output prefix>.ldset.
+.TP
+\fB\-\-set\-max\fR <ct>
+: Adjust set test maximum # of significant variants
+considered per set (default 5).
+.TP
+\fB\-\-set\-test\-lambda\fR <v>
+: Specify genomic control correction for set test.
+.TP
+\fB\-\-border\fR <kbs>
+: Extend \fB\-\-annotate\fR range intervals by given # kbs.
+.HP
+\fB\-\-annotate\-snp\-field\fR <nm> : Set \fB\-\-annotate\fR variant ID field name.
+.HP
+\fB\-\-clump\-p1\fR <pval> : Set \fB\-\-clump\fR index var. p\-value ceiling (default 1e\-4).
+.HP
+\fB\-\-clump\-p2\fR <pval> : Set \fB\-\-clump\fR secondary p\-value threshold (default 0.01).
+.TP
+\fB\-\-clump\-r2\fR <r^2>
+: Set \fB\-\-clump\fR r^2 threshold (default 0.5).
+.TP
+\fB\-\-clump\-kb\fR <kbs>
+: Set \fB\-\-clump\fR kb radius (default 250).
+.TP
+\fB\-\-clump\-snp\-field\fR <n...>
+: Set \fB\-\-clump\fR variant ID field name (default
+\&'SNP'). With multiple field names, earlier names
+take precedence over later ones.
+.TP
+\fB\-\-clump\-field\fR <name...>
+: Set \fB\-\-clump\fR p\-value field name (default 'P').
+.TP
+\fB\-\-clump\-allow\-overlap\fR
+: Let \fB\-\-clump\fR non\-index vars. join multiple clumps.
+.TP
+\fB\-\-clump\-verbose\fR
+: Request extended \fB\-\-clump\fR report.
+.TP
+\fB\-\-clump\-annotate\fR <hdr...> : Include named extra fields in \fB\-\-clump\-verbose\fR and
+\fB\-\-clump\-best\fR reports. (Field names can be
+separated with spaces or commas.)
+.TP
+\fB\-\-clump\-range\fR <filename>
+: Report overlaps between clumps and regions.
+.HP
+\fB\-\-clump\-range\-border\fR <kb> : Stretch regions in \fB\-\-clump\-range\fR file.
+.TP
+\fB\-\-clump\-index\-first\fR
+: Extract \fB\-\-clump\fR index vars. from only first file.
+.TP
+\fB\-\-clump\-replicate\fR
+: Exclude clumps which contain secondary results
+from only one file.
+.TP
+\fB\-\-clump\-best\fR
+: Report best proxy for each \fB\-\-clump\fR index var.
+.HP
+\fB\-\-meta\-analysis\-chr\-field\fR <n...> : Set \fB\-\-meta\-analysis\fR chromosome, variant
+.TP
+\fB\-\-meta\-analysis\-snp\-field\fR <n...>
+ID, position, A1/A2 allele, p\-value,
+.TP
+\fB\-\-meta\-analysis\-bp\-field\fR <n...>
+standard error, and/or effective sample
+.TP
+\fB\-\-meta\-analysis\-a1\-field\fR <n...>
+size field names.
+.TP
+\fB\-\-meta\-analysis\-a2\-field\fR <n...>
+Defaults are 'CHR', 'SNP', 'BP', 'A1',
+.TP
+\fB\-\-meta\-analysis\-p\-field\fR <n...>
+\&'A2', 'P', 'SE', and 'NMISS',
+.TP
+\fB\-\-meta\-analysis\-se\-field\fR <n...>
+respectively. When multiple parameters
+.TP
+\fB\-\-meta\-analysis\-ess\-field\fR <n...>
+are given to these flags, earlier names
+take precedence over later ones.
+Note that, if the numbers of cases and
+controls are unequal, effective sample
+size should be
+.IP
+4 / (1/<# cases> + 1/<# controls>).
+.TP
+\fB\-\-meta\-analysis\-report\-dups\fR
+: When a variant appears multiple times in
+in the same file, report that.
+.TP
+\fB\-\-gene\-list\-border\fR <kbs>
+: Extend \fB\-\-gene\-report\fR regions by given # of kbs.
+.TP
+\fB\-\-gene\-subset\fR <filename>
+: Specify gene name subset for \fB\-\-gene\-report\fR.
+.TP
+\fB\-\-gene\-report\-snp\-field\fR <> : Set \fB\-\-gene\-report\fR variant ID field name (default
+\&'SNP'). Only relevant with \fB\-\-extract\fR.
+.TP
+\fB\-\-gap\fR <kbs>
+: Set "\-\-fast\-epistasis case\-only" min. gap (default 1000).
+.TP
+\fB\-\-epi1\fR <p\-value> : Set \fB\-\-[fast\-]epistasis\fR reporting threshold (default
+5e\-6 for 'boost', 1e\-4 otherwise).
+.HP
+\fB\-\-epi2\fR <p\-value> : Set threshold for contributing to SIG_E count (def. 0.01).
+.TP
+\fB\-\-je\-cellmin\fR <n> : Set required number of observations per 3x3x2 contingency
+table cell for joint\-effects test (default 5).
+.HP
+\fB\-\-q\-score\-range\fR <range file> <data file> [i] [j] ['header'] :
+.IP
+Apply \fB\-\-score\fR to subset(s) of variants in the primary score list based
+on e.g. p\-value ranges.
+* The first file should have range labels in the first column, p\-value
+.IP
+lower bounds in the second column, and upper bounds in the third column.
+Lines with too few entries, or nonnumeric values in the second or third
+column, are ignored.
+.IP
+* The second file should contain a variant ID and a p\-value on each
+.TP
+nonempty line (except possibly the first).
+Variant IDs are read from
+.IP
+column #i and p\-values are read from column #j, where i defaults to 1 and
+j defaults to i+1. The 'header' modifier causes the first nonempty line
+of this file to be skipped.
+.TP
+\fB\-\-R\-port\fR <port #>
+: Connect to Rserve on a port other than 6311.
+.TP
+\fB\-\-R\-host\fR <host>
+: Connect to Rserve host.
+.TP
+\fB\-\-R\-socket\fR <sock>
+: Connect to Rserve socket.
+.TP
+\fB\-\-parallel\fR <k> <n> : Divide the output matrix into n pieces, and only compute
+the kth piece. The primary output file will have the
+piece number included in its name, e.g. plink.rel.13 or
+plink.rel.13.gz if k is 13. Concatenating these files
+in order will yield the full matrix of interest. (Yes,
+this can be done before unzipping.)
+N.B. This generally cannot be used to directly write a
+symmetric square matrix. Choose square0 or triangle
+shape instead, and postprocess as necessary.
+.TP
+\fB\-\-memory\fR <val>
+: Set size, in MB, of initial workspace malloc attempt.
+(Practically mandatory when using GNU parallel.)
+.TP
+\fB\-\-threads\fR <val>
+: Set maximum number of concurrent threads.
+This has one known limitation: some BLAS/LAPACK linear
+algebra operations are multithreaded in a way that PLINK
+cannot control. If this is problematic, you should
+recompile against single\-threaded BLAS/LAPACK.
+.TP
+\fB\-\-d\fR <char>
+: Change variant/covariate range delimiter (normally '\-').
+.TP
+\fB\-\-seed\fR <val...>
+: Set random number seed(s). Each value must be an
+integer between 0 and 4294967295 inclusive.
+.TP
+\fB\-\-perm\-batch\-size\fR <val> : Set number of permutations per batch for some
+permutation tests.
+.HP
+\fB\-\-output\-min\-p\fR <p> : Specify minimum p\-value to write to reports.
+.TP
+\fB\-\-debug\fR
+: Use slower, more crash\-resistant logging method.
+.PP
+Primary methods paper:
+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.
+.PP
+For further documentation and support, consult the main webpage
+(https://www.cog\-genomics.org/plink/1.9 ) and/or the mailing list
+(https://groups.google.com/d/forum/plink2\-users ).
+.SH "SEE ALSO"
+The full documentation for
+.B PLINK v1.90b6.16 64-bit (19 Feb
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B PLINK v1.90b6.16 64-bit (19 Feb
+programs are properly installed at your site, the command
+.IP
+.B info PLINK v1.90b6.16 64-bit (19 Feb
+.PP
+should give you access to the complete manual.
=====================================
debian/rules
=====================================
@@ -17,12 +17,16 @@ override_dh_auto_clean:
override_dh_auto_build:
dh_auto_build
mv plink plink1.9
- help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1
+# help2man 1.47.13 is not able anymore do generate a clean manpage for plink1.9
+# which lead to several lintian warnings and more annoying the auto-generated
+# manpage is installed by debhelper in the wrong section due to
+# https://bugs.debian.org/958343
+# help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1
override_dh_auto_install:
override_dh_installman:
- dh_installman plink1.9.1
+ dh_installman debian/plink1.9.1
override_dh_installchangelogs:
dh_installchangelogs debian/upstream.docs/upstream.changelog
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012
--
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/-/commit/391c3a96b4532fd9432ae9693b685d0113cda012
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