[med-svn] [Git][med-team/plink2][master] 2 commits: Do not generate manpage for plink2 with help2man
Dylan Aïssi
gitlab at salsa.debian.org
Tue Apr 21 10:30:25 BST 2020
Dylan Aïssi pushed to branch master at Debian Med / plink2
Commits:
c0beb560 by Dylan Aïssi at 2020-04-21T11:25:02+02:00
Do not generate manpage for plink2 with help2man
- - - - -
01274352 by Dylan Aïssi at 2020-04-21T11:29:58+02:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- + debian/plink2.1
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,10 @@
-plink2 (2.00~a3-200409+dfsg-1) UNRELEASED; urgency=medium
+plink2 (2.00~a3-200409+dfsg-1) unstable; urgency=medium
* New upstream release.
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
- -- Dylan Aïssi <daissi at debian.org> Fri, 27 Mar 2020 08:44:27 +0100
+ -- Dylan Aïssi <daissi at debian.org> Tue, 21 Apr 2020 11:29:42 +0200
plink2 (2.00~a3-200217+dfsg-1) unstable; urgency=medium
=====================================
debian/plink2.1
=====================================
@@ -0,0 +1,2544 @@
+.TH PLINK "1" "March 2020" "PLINK v2.00a3 64-bit (9 Apr 2020)" "User Commands"
+.SH NAME
+PLINK \- whole genome SNP analysis
+.SH DESCRIPTION
+PLINK v2.00a3 64\-bit (9 Apr 2020) www.cog\-genomics.org/plink/2.0/
+(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 arguments of the
+.IP
+specified type.
+.IP
+* A "column set descriptor" is either
+.IP
+1. a comma\-separated sequence of column set names; this is interpreted as
+.IP
+the full list of column sets to include.
+.IP
+2. a comma\-separated sequence of column set names, all preceded by '+' or
+.IP
+\&'\-'; this is interpreted as a list of changes to the default.
+.IP
+plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
+plink2 \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:
+.TP
+\fB\-\-pfile\fR <prefix> ['vzs']
+: Specify .pgen + .pvar[.zst] + .psam prefix.
+.TP
+\fB\-\-pgen\fR <filename>
+: Specify full name of .pgen/.bed file.
+.TP
+\fB\-\-pvar\fR <filename>
+: Specify full name of .pvar/.bim file.
+.TP
+\fB\-\-psam\fR <filename>
+: Specify full name of .psam/.fam file.
+.TP
+\fB\-\-bfile\fR
+<prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.
+.HP
+\fB\-\-bpfile\fR <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.
+.TP
+\fB\-\-keep\-autoconv\fR ['vzs']
+: When importing non\-PLINK\-binary data, don't
+delete autogenerated fileset at end of run.
+.TP
+\fB\-\-no\-fid\fR
+: .fam file does not contain column 1 (family ID).
+.TP
+\fB\-\-no\-parents\fR
+: .fam file does not contain columns 3\-4 (parents).
+.TP
+\fB\-\-no\-sex\fR
+: .fam file does not contain column 5 (sex).
+.HP
+\fB\-\-vcf\fR <filename> ['dosage='<field>]
+.HP
+\fB\-\-bcf\fR <filename> ['dosage='<field>] :
+.IP
+Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.
+* These can be used with \fB\-\-psam\fR/\-\-fam.
+* By default, dosage information is not imported. To import the GP field
+.IP
+(must be VCFv4.3\-style 0..1, one probability per possible genotype), add
+\&'dosage=GP' (or 'dosage=GP\-force', see below). To import Minimac3\-style
+DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else
+for now) causes the named field to be interpreted as a Minimac3\-style
+dosage.
+Note that, in the dosage=GP case, PLINK 2 collapses the probabilities
+down to dosages; you cannot use PLINK 2 to losslessly convert VCF
+FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2
+now errors out when dosage=GP is used on a file with a FORMAT:DS header
+line and \fB\-\-import\-dosage\-certainty\fR wasn't specified, since dosage=DS
+extracts the same information more quickly in this situation. You can
+suppress this error with 'dosage=GP\-force'.
+In all of these cases, hardcalls are regenerated from scratch from the
+dosages. As a consequence, variants with no GT field can now be
+imported; they will be assumed to contain only diploid calls when HDS is
+also absent.
+.HP
+\fB\-\-data\fR <filename prefix> <REF/ALT mode> ['gzs']
+.HP
+\fB\-\-bgen\fR <filename> <REF/ALT mode> ['snpid\-chr']
+.HP
+\fB\-\-gen\fR <filename> <REF/ALT mode>
+.HP
+\fB\-\-sample\fR <filename> :
+.TP
+Specify an Oxford\-format dataset to import.
+\fB\-\-data\fR specifies a .gen[.zst]
+.IP
++ .sample pair, while \fB\-\-bgen\fR specifies a BGEN v1.1+ file.
+* If a BGEN v1.2+ file contains sample IDs, it may be imported without a
+.IP
+companion .sample file.
+.IP
+* With 'snpid\-chr', chromosome codes are read from the 'SNP ID' field
+.IP
+instead of the usual chromosome field.
+.IP
+* The following REF/ALT modes are supported:
+.IP
+\&'ref\-first': The first allele for each variant is REF.
+\&'ref\-last': The last allele for each variant is REF.
+\&'ref\-unknown': The last allele for each variant is treated as
+.IP
+provisional\-REF.
+.HP
+\fB\-\-haps\fR <filename> [{ref\-first | ref\-last}]
+.HP
+\fB\-\-legend\fR <filename> <chr code> :
+.IP
+Specify .haps [+ .legend] file(s) to import.
+* When \fB\-\-legend\fR is specified, it's assumed that the \fB\-\-haps\fR file doesn't
+.IP
+contain header columns.
+.TP
+* On chrX, the second male column may contain dummy '\-' entries.
+(However,
+.IP
+PLINK 2 currently cannot handle omitted male columns.)
+.IP
+* If not used with \fB\-\-sample\fR, new sample IDs are of the form 'per#/per#'.
+.TP
+\fB\-\-map\fR <filename>
+: Specify full name of .map file.
+.HP
+\fB\-\-import\-dosage\fR <allele dosage file> ['noheader'] ['id\-delim='<char>]
+.IP
+['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1']
+['format='<m>] [{ref\-first | ref\-last}]
+['single\-chr='<code>] ['chr\-col\-num='<#>]
+['pos\-col\-num='<#>] :
+.IP
+Specify PLINK 1.x\-style dosage file to import.
+* You must also specify a companion .psam/.fam file.
+* By default, PLINK assumes that the file contains a header line, which has
+.IP
+\&'SNP' in (1\-based) 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. FID/IID are normally assumed to be separate tokens, but if
+they're merged into a single token you can specify the delimiter with
+\&'id\-delim='.) If such a header line is not present, use the 'noheader'
+modifier; samples will then be assumed to appear in the same order as
+they do in the .psam/.fam file.
+.TP
+* You may specify a companion .map file.
+If you do not,
+.IP
+* 'single\-chr=' can be used to specify that all variants are on the named
+.TP
+chromosome.
+Otherwise, you can use 'chr\-col\-num=' to read chromosome
+.IP
+codes from the given (1\-based) column number.
+.IP
+* 'pos\-col\-num=' causes bp coordinates to be read from the given column
+.IP
+number.
+.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
+indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het
+likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2.
+\&'format=infer' (the default) infers the format from the number of columns
+in the first nonheader line.
+.HP
+\fB\-\-dummy\fR <sample ct> <SNP ct> [missing dosage freq] [missing pheno freq]
+.IP
+[{acgt | 1234 | 12}] ['pheno\-ct='<count>] ['scalar\-pheno']
+['dosage\-freq='<rate>]
+.IP
+This generates a fake input dataset with the specified number of samples
+and SNPs.
+* By default, the missing dosage and phenotype frequencies are zero.
+.IP
+These can be changed by providing 3rd and 4th numeric arguments.
+.IP
+* By default, allele codes are As and Bs; this can be changed with the
+.IP
+\&'acgt', '1234', or '12' modifier.
+.TP
+* By default, one binary phenotype is generated.
+\&'pheno\-ct=' can be used
+.IP
+to change the number of phenotypes, and 'scalar\-pheno' causes these
+phenotypes to be normally distributed scalars.
+.TP
+* By default, all (nonmissing) dosages are in {0,1,2}.
+To make some of
+.TP
+them take on decimal values, use 'dosage\-freq='.
+(These dosages are
+.IP
+affected by \fB\-\-hard\-call\-threshold\fR and \fB\-\-dosage\-erase\-threshold\fR.)
+.TP
+\fB\-\-fa\fR <filename>
+: Specify full name of reference FASTA file.
+.PP
+Output files have names of the form 'plink2.<extension>' by default. You can
+change the 'plink2' 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\-\-rm\-dup\fR [mode] ['list']
+.IP
+Remove all but one instance of each duplicate\-ID variant (ignoring the
+missing ID), and (with the 'list' modifier) write a list of duplicated IDs
+to <output prefix>.rmdup.list.
+The following modes of operation are supported:
+* 'error' (default) causes this to error out when there's a genotype data
+.TP
+or other mismatch between the records.
+A list of affected IDs is written
+.IP
+to <output prefix>.rmdup.mismatch.
+.IP
+* 'retain\-mismatch' causes all instances of a duplicate\-ID variant to be
+.IP
+retained when there's a genotype data or variant info mismatch; otherwise
+one instance is kept. The .rmdup.mismatch file is also written.
+.IP
+* 'exclude\-mismatch' removes all instances of duplicate\-ID mismatched
+.IP
+variants instead.
+.IP
+* 'exclude\-all' causes all instances of duplicate\-ID variants to be
+.IP
+removed, even when the actual records are identical.
+.IP
+* 'force\-first' causes only the first instance of duplicate\-ID variants to
+.IP
+be kept, under all circumstances.
+.HP
+\fB\-\-make\-pgen\fR ['vzs'] ['format='<code>] ['trim\-alts'] ['erase\-phase']
+.IP
+['erase\-dosage'] ['pvar\-cols='<col set descriptor>]
+['psam\-cols='<col set descriptor>]
+.HP
+\fB\-\-make\-bpgen\fR ['vzs'] ['format='<code>] ['trim\-alts'] ['erase\-phase']
+.IP
+['erase\-dosage']
+.HP
+\fB\-\-make\-bed\fR ['vzs'] ['trim\-alts']
+.IP
+Create a new PLINK 2 binary fileset (\fB\-\-make\-pgen\fR = .pgen + .pvar[.zst] +
+\&.psam, \fB\-\-make\-bpgen\fR = .pgen + .bim[.zst] + .fam).
+* Unlike the automatic text\-to\-binary converters (which only heed
+.IP
+chromosome filters), this supports all of PLINK's filtering flags.
+.IP
+* The 'vzs' modifier causes the variant file (.pvar/.bim) to be
+.IP
+Zstd\-compressed.
+.IP
+* The 'format' modifier requests an uncompressed fixed\-variant\-width .pgen
+.TP
+file.
+(These do not directly support multiallelic variants.) The
+.IP
+following format code is currently supported:
+.IP
+2: just like .bed, except with an extended (12\-byte instead of 3\-byte)
+.IP
+header containing variant/sample counts, and rotated genotype codes
+(00 = hom ref, 01 = het, 10 = hom alt, 11 = missing).
+.IP
+* The 'erase\-phase' and 'erase\-dosage' modifiers prevent phase and dosage
+.IP
+information from being written to the new .pgen.
+.IP
+* The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT.
+.IP
+Supported optional .pvar column sets are:
+.IP
+xheader: All ## header lines (yeah, this is technically not a column),
+.IP
+except for possibly FILTER/INFO definitions when those
+column(s) have been removed. Without this, only the #CHROM
+header line is kept.
+.IP
+vcfheader: xheader, with additions to make it a valid VCF header.
+maybequal: QUAL. Omitted if all remaining values are missing.
+qual: Force QUAL column to be written even when empty.
+maybefilter: FILTER. Omitted if all remaining values are missing.
+filter: Force FILTER column to be written even when empty.
+maybeinfo: INFO. Omitted if all remaining values are missing, or if
+.IP
+INFO:PR is the only subfield.
+.IP
+info: Force INFO column to be written.
+maybecm: Centimorgan coordinate. Omitted if all remaining values = 0.
+cm: Force CM column to be written even when empty.
+.IP
+The default is xheader,maybequal,maybefilter,maybeinfo,maybecm.
+.IP
+* Supported column sets for the .psam file are:
+.TP
+maybefid: Family ID, '0' = missing.
+Omitted if all values missing.
+.IP
+fid: Force FID column to be written even when empty.
+maybesid: Source ID, '0' = missing. Omitted if all values missing.
+sid: Force SID column to be written even when empty.
+maybeparents: Father and mother IIDs. Omitted if all values missing.
+parents: Force PAT and MAT columns to be written even when empty.
+sex: '1' = male, '2' = female, 'NA' = missing.
+pheno1: First active phenotype. If none, all column entries are set to
+.IP
+the \fB\-\-output\-missing\-phenotype\fR string.
+.TP
+phenos: All active phenotypes, if any.
+(Can be combined with pheno1 to
+.IP
+force at least one phenotype column to be written.)
+.IP
+The default is maybefid,maybesid,maybeparents,sex,phenos.
+.HP
+\fB\-\-make\-just\-pvar\fR ['zs'] ['cols='<column set descriptor>]
+.HP
+\fB\-\-make\-just\-psam\fR ['cols='<column set descriptor>]
+.HP
+\fB\-\-make\-just\-bim\fR ['zs']
+.HP
+\fB\-\-make\-just\-fam\fR
+.IP
+Variants of \fB\-\-make\-pgen\fR/\-\-make\-bed which only write a new variant or sample
+file. These don't always require an input genotype file.
+USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary
+genotype data and your sample/variant indexes if you use these commands
+improperly. If you have any doubt, stick with \fB\-\-make\-[b]pgen\fR/\-\-make\-bed.
+.HP
+\fB\-\-export\fR <output format(s)...> [{01 | 12}] ['bgz'] ['id\-delim='<char>]
+.IP
+['id\-paste='<column set descriptor>] ['include\-alt']
+['omit\-nonmale\-y'] ['spaces'] ['vcf\-dosage='<field>] ['ref\-first']
+['bits='<#>]
+.TP
+Create a new fileset with all filters applied.
+The following output
+.IP
+formats are supported:
+(actually, only A, AD, A\-transpose, bcf, bgen\-1.x, haps, hapslegend,
+ind\-major\-bed, oxford, and vcf are implemented for now)
+* '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.
+* 'bgen\-1.x': Oxford\-format .bgen + .sample. For v1.2/v1.3, sample
+.IP
+identifiers are stored in the .bgen (with id\-delim and
+id\-paste settings applied), and default precision is 16\-bit
+(use the 'bits' modifier to reduce this).
+.IP
+* '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 #>.phase.inp filename extensions.
+.TP
+* 'fastphase\-1chr': Single .phase.inp file.
+Does not support
+.IP
+multiple chromosomes.
+.TP
+* 'haps', 'hapslegend': Oxford\-format .haps + .sample[ + .legend].
+All
+.TP
+data must be biallelic and phased.
+When the 'bgz'
+.TP
+modifier is present, the .haps file is
+block\-gzipped.
+.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
+* 'ind\-major\-bed': PLINK 1 sample\-major .bed (+ .bim + .fam).
+* 'lgen': PLINK 1 long\-format (.lgen + .fam + .map), loadable with \fB\-\-lfile\fR.
+* 'lgen\-ref': .lgen + .fam + .map + .ref, loadable with \fB\-\-lfile\fR +
+.IP
+\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.
+When the 'bgz' modifier is
+.IP
+present, the .gen file is block\-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
+.IP
+\fB\-\-tfile\fR.
+.TP
+* 'vcf',
+: VCF (default version 4.3). If PAR1 and PAR2 are present,
+.TP
+\&'vcf\-4.2',
+they are automatically merged with chrX, with proper
+.TP
+\&'bcf',
+handling of chromosome codes and male ploidy.
+.TP
+\&'bcf\-4.2'
+When the 'bgz' modifier is present, the VCF file is
+block\-gzipped. (This always happens with BCF output.)
+The 'id\-paste' modifier controls which .psam columns are
+used to construct sample IDs (choices are maybefid, fid,
+iid, maybesid, and sid; default is maybefid,iid,maybesid),
+while the 'id\-delim' modifier sets the character between the
+ID pieces (default '_').
+Genotypes are always exported. If you want to export a
+sites\-only VCF instead, see \fB\-\-make\-pgen\fR/\-\-make\-just\-pvar's
+\&'vcfheader' column set.
+Dosages are not exported unless the 'vcf\-dosage=' modifier
+is present. The following five dosage export modes are
+supported:
+\&'GP': genotype posterior probabilities (v4.3 only).
+\&'DS': Minimac3\-style dosages, omitted for hardcalls.
+\&'DS\-force': Minimac3\-style dosages, never omit.
+\&'HDS': Minimac3\-style phased dosages, omitted for hardcalls
+.TP
+and unphased calls.
+Also includes 'DS' output.
+.IP
+\&'HDS\-force': Always report DS and HDS.
+.IP
+In addition,
+* The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles
+.IP
+to be coded as '2', while '01' maps alt1 \-> 0 and ref \-> 1.
+.IP
+* The 'spaces' modifier makes the output space\-delimited instead of
+.IP
+tab\-delimited, whenever both are permitted.
+.IP
+* For biallelic formats where it's unspecified whether the reference/major
+.IP
+allele should appear first or second, \fB\-\-export\fR defaults to second for
+compatibility with PLINK 1.9. Use 'ref\-first' to change this.
+(Note that this doesn't apply to the 'A', 'AD', and 'A\-transpose'
+formats; use \fB\-\-export\-allele\fR to control which alleles are counted there.)
+.HP
+\fB\-\-freq\fR ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins\-only']
+.IP
+['refbins='<comma\-separated bin boundaries> | 'refbins\-file='<file>]
+['alt1bins='<comma\-separated bin boundaries> | 'alt1bins\-file='<file>]
+.TP
+Empirical allele frequency report.
+By default, only founders are
+.TP
+considered.
+Dosages are taken into account (e.g. heterozygous haploid
+.IP
+calls count as 0.5).
+Supported column sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+reffreq: Reference allele frequency/dosage.
+alt1freq: Alt1 frequency/dosage.
+altfreq: Comma\-separated frequencies/dosages for all alternate alleles.
+freq: Similar to altfreq, except ref is also included at the start.
+eq: Comma\-separated <allele>=<freq> for all present alleles. (If no
+.IP
+alleles are present, the column contains a single '.'.)
+.IP
+eqz: Same as eq, except zero\-counts are included.
+alteq/alteqz: Same as eq/eqz, except reference allele is omitted.
+numeq: 0=<freq>,1=<freq>, etc. Zero\-counts are omitted.
+altnumeq: Same as numeq, except reference allele is omitted.
+machr2: Unphased MaCH imputation quality metric.
+minimac3r2: Phased Minimac3 imputation quality.
+nobs: Number of allele observations.
+.IP
+The default is chrom,ref,alt,altfreq,nobs.
+Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with
+\&'counts') file(s) are generated when 'refbins='/'refbins\-file=' or
+\&'alt1bins='/'alt1bins\-file=' is present; these report the total number of
+frequencies or counts in each left\-closed, right\-open interval. (If you
+only want these histogram(s), and not the main report, add 'bins\-only'.)
+.HP
+\fB\-\-geno\-counts\fR ['zs'] ['cols='<column set descriptor>]
+.IP
+Variant\-based hardcall genotype count report (considering both alleles
+simultaneously in the diploid case). Nonfounders are now included; use
+\fB\-\-keep\-founders\fR if this is a problem. Heterozygous haploid calls are
+treated as missing.
+Supported column sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+homref: Homozygous\-ref count.
+refalt1: Heterozygous ref\-alt1 count.
+refalt: Comma\-separated het ref\-altx counts.
+homalt1: Homozygous\-alt1 count.
+altxy: Comma\-separated altx\-alty counts, in (1/1)\-(1/2)\-(2/2)\-(1/3)\-...
+.IP
+order.
+.IP
+xy: Similar to altxy, except the reference allele is treated as alt0,
+.IP
+and the sequence starts (0/0)\-(0/1)\-(1/1)\-(0/2)\-...
+.IP
+hapref: Haploid\-ref count.
+hapalt1: Haploid\-alt1 count.
+hapalt: Comma\-separated haploid\-altx counts.
+hap: Similar to hapalts, except ref is also included at the start.
+numeq: 0/0=<hom ref ct>,0/1=<het ref\-alt1>,1/1=<hom alt1>,...,0=<hap ref>
+.TP
+etc.
+Zero\-counts are omitted. (If all genotypes are missing, the
+.IP
+column contains a single '.'.)
+.IP
+missing: Number of missing genotypes.
+nobs: Number of (nonmissing) genotype observations.
+.IP
+The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing.
+.HP
+\fB\-\-sample\-counts\fR ['zs'] ['cols='<column set descriptor>]
+.IP
+Sample\-based hardcall genotype count report.
+* Unknown\-sex samples are treated as female.
+* Heterozygous haploid calls (MT included) are treated as missing.
+* As with other PLINK 2 commands, SNPs that have not been left\-normalized
+.TP
+are counted as non\-SNP non\-symbolic.
+(Use e.g. \fB\-\-normalize\fR when that's a
+.IP
+problem.)
+.IP
+* Supported column sets are:
+.IP
+maybefid: FID, if that column was present in the input.
+fid: Force FID column to be written even when absent in the input.
+(IID is always present, and positioned here.)
+maybesid: SID, if that column was present in the input.
+sid: Force SID column to be written even when absent in the input.
+sex: '1' = male, '2' = female, 'NA' = missing.
+hom: Homozygous genotype count.
+homref: Homozygous\-ref genotype count.
+homalt: Homozygous\-alt genotype count.
+homaltsnp: Homozygous\-alt SNP count.
+het: Heterozygous genotype count.
+refalt: Heterozygous ref\-altx genotype count.
+het2alt: Heterozygous altx\-alty genotype count.
+hetsnp: Heterozygous SNP count.
+dipts: Diploid SNP transition count.
+ts: SNP transition count (excluding chrY for females).
+diptv: Diploid SNP transversion count.
+tv: SNP transversion count.
+dipnonsnpsymb: Diploid non\-SNP, non\-symbolic count.
+nonsnpsymb: Non\-SNP, non\-symbolic count.
+symbolic: Symbolic variant count.
+nonsnp: Non\-SNP count.
+dipsingle: Number of singletons relative to this dataset, across just
+.TP
+diploid calls.
+(Note that if the ALT allele in a chrX
+.IP
+biallelic variant appears in exactly one female and one
+male, that counts as a singleton for just the female.)
+.IP
+single: Number of singletons relative to this dataset.
+haprefwfemaley: Haploid\-ref count, counting chrY for everyone.
+hapref: Haploid\-ref count, excluding chrY for females.
+hapaltwfemaley: Haploid\-alt count, counting chrY for everyone.
+hapalt: Haploid\-alt count, excluding chrY for females.
+missingwfemaley: Missing call count, counting chrY for everyone.
+missing: Missing call count, excluding chrY for females.
+.IP
+The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv,
+dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley.
+.IP
+* The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb',
+.IP
+\&'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous
+altx\-alty call separately, since they can be of different subtypes.
+(I.e. if they are of the same subtype, the corresponding count is
+incremented by 2.) As a consequence, these columns are unaffected by
+variant split/join.
+.HP
+\fB\-\-missing\fR ['zs'] [{sample\-only | variant\-only}]
+.IP
+['scols='<column set descriptor>] ['vcols='<column set descriptor>]
+.IP
+Generate sample\- and variant\-based missing data reports (or just one report
+if 'sample\-only'/'variant\-only' is specified).
+As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats.
+Supported column sets in the sample\-based report are:
+.IP
+maybefid: FID, if that column was present in the input.
+fid: Force FID column to be written even when absent in the input.
+(IID is always present, and positioned here.)
+maybesid: SID, if that column was present in the input.
+sid: Force SID column to be written even when absent in the input.
+misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no
+.IP
+phenotypes are loaded.
+.TP
+missphenos: A Y/N column for each loaded phenotype.
+(Can be combined
+.IP
+with misspheno1 to force at least one such column.)
+.IP
+nmissdosage: Number of missing dosages.
+nmiss: Number of missing hardcalls, not counting het haploids.
+nmisshh: Number of missing hardcalls, counting het haploids.
+hethap: Number of heterozygous haploid hardcalls.
+nobs: Denominator (male count on chrY, otherwise total sample count).
+fmissdosage: Missing dosage rate.
+fmiss: Missing hardcall rate, not counting het haploids.
+fmisshh: Missing hardcall rate, counting het haploids.
+.IP
+The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss.
+Supported column sets in the variant\-based report are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+nmissdosage: Number of missing dosages.
+nmiss: Number of missing hardcalls, not counting het haploids.
+nmisshh: Number of missing hardcalls, counting het haploids.
+hethap: Number of heterozygous haploid calls.
+nobs: Number of potentially valid calls.
+fmissdosage: Missing dosage rate.
+fmiss: Missing hardcall rate, not counting het haploids.
+fmisshh: Missing hardcall rate, counting het haploids.
+fhethap: Heterozygous haploid rate.
+.IP
+The default is chrom,nmiss,nobs,fmiss.
+.HP
+\fB\-\-hardy\fR ['zs'] ['midp'] ['redundant'] ['cols='<column set descriptor>]
+.IP
+Hardy\-Weinberg exact test p\-value report(s).
+* By default, only founders are considered; change this with \fB\-\-nonfounders\fR.
+* chrX is now omitted from the main <output prefix>.hardy report. Instead,
+.IP
+(if present) it gets its own <output prefix>.hardy.x report based on the
+method described in Graffelman J, Weir BS (2016) Hardy\-Weinberg
+equilibrium and the X chromosome.
+.IP
+* For variants with k alleles where k>2, k separate 'biallelic' tests are
+.TP
+performed, each reported on its own line.
+However, biallelic variants
+.IP
+are normally reported on a single line, since the counts/frequencies
+would be mirror\-images and the p\-values would be the same. You can add
+the 'redundant' modifier to force biallelic variant results to be
+reported on two lines for parsing convenience.
+.IP
+* There is currently no special handling of case/control phenotypes.
+Supported column sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+(A1 is always present, and positioned here.)
+ax: Non\-A1 allele(s), comma\-separated.
+gcounts: Hom\-A1 count, total number of het\-A1 calls, and total number of
+.TP
+nonmissing calls with no copies of A1.
+On chrX, these are
+.IP
+followed by male A1 and male non\-A1 counts.
+.IP
+gcount1col: gcounts values in a single comma\-separated column.
+hetfreq: Observed and expected het\-A1 frequencies.
+sexaf: Female and male A1 observed allele frequencies (chrX only).
+femalep: Female\-only p/midp\-value (chrX only).
+p: Hardy\-Weinberg equilibrium exact test p/midp\-value.
+.IP
+The default is chrom,ax,gcounts,hetfreq,sexaf,p.
+.HP
+\fB\-\-indep\-pairwise\fR <window size>['kb'] [step size (variant ct)]
+.IP
+<unphased\-hardcall\-r^2 threshold>
+.IP
+Generate a list of variants in approximate linkage equilibrium.
+* For multiallelic variants, major allele counts are used in the r^2
+.IP
+computation.
+.IP
+* With the 'kb' modifier, the window size is in kilobase instead of variant
+.TP
+count units.
+(Pre\-'kb' space is optional, i.e.
+.IP
+"\-\-indep\-pairwise 500 kb 0.5" and "\-\-indep\-pairwise 500kb 0.5" have the
+same effect.)
+.IP
+* The step size now defaults to 1 if it's unspecified, and *must* be 1 if
+.IP
+the window is in kilobase units.
+.IP
+* Note that you need to rerun PLINK using \fB\-\-extract\fR or \fB\-\-exclude\fR on the
+.IP
+\&.prune.in/.prune.out file to apply the list to another computation... and
+as with other applications of \fB\-\-extract\fR/\-\-exclude, duplicate variant IDs
+are a problem. \fB\-\-indep\-pairwise\fR still runs to completion for now when
+duplicate variant IDs are present, but that will become an error in alpha
+3.
+.HP
+\fB\-\-ld\fR <variant ID> <variant ID> ['dosage'] ['hwe\-midp']
+.IP
+This displays diplotype frequencies, r^2, and D' for a single pair of
+variants.
+* For multiallelic variants, major allele counts/dosages are used.
+* Phase information is used when both variants are on the same chromosome.
+* When there is at least one sample with unphased het calls for both
+.IP
+variants, diplotype frequencies are estimated using the Hill equation.
+If there are multiple biologically possible local maxima, all are
+displayed, along with HWE exact test statistics.
+.TP
+* By default, only hardcalls are considered.
+Add the 'dosage' modifier if
+.TP
+you want dosages to be taken into account.
+(In the diploid case, an
+.IP
+unphased dosage of x is interpreted as P(0/0) = 1 \- x, P(0/1) = x when x
+is in 0..1.)
+.HP
+\fB\-\-sample\-diff\fR ['id\-delim='<char>] ['dosage' | 'dosage='<tolerance>]
+.IP
+['include\-missing'] [{pairwise | counts\-only}]
+['fname\-id\-delim='<c>] ['zs'] ['cols='<column set descriptor>]
+['counts\-cols='<column set descriptor>]
+{base= | ids=}<sample ID> [other sample ID(s)...]
+.HP
+\fB\-\-sample\-diff\fR ['id\-delim='<char>] ['dosage' | 'dosage='<tolerance>]
+.IP
+['include\-missing'] [{pairwise | counts\-only}]
+['fname\-id\-delim='<c>] ['zs'] ['cols='<column set descriptor>]
+['counts\-cols='<column set descriptor>] file=<ID\-pair file>
+.IP
+(alias: \fB\-\-sdiff\fR)
+Report discordances and discordance\-counts between pairs of samples. If
+chrX or chrY is present, sex must be defined and consistent.
+* There are three ways to specify which sample pairs to compare. To
+.IP
+compare a single baseline sample against some others, start the
+(space\-delimited) sample ID list with 'base='. To perform an all\-vs.\-all
+comparison, start it with 'ids=' instead. To compare sample pairs listed
+in a file, use 'file='.
+Note that 'base='/'ids='/'file=' must be positioned after all modifiers.
+.IP
+* Sample IDs are interpreted as if they were in a VCF header line, with
+.IP
+\&'id\-delim=' having the usual effect.
+.TP
+* By default, comparisons are based on hardcalls.
+Use 'dosage' to compare
+.IP
+dosages instead; you can combine this with a tolerance in [0, 0.5).
+.IP
+* By default, if one genotype is missing and the other isn't, that doesn't
+.IP
+count as a difference; this can be changed with 'include\-missing'.
+.IP
+* By default, a single main report is written to
+.TP
+<output prefix>[.<base ID>].sdiff.
+To write separate pairwise
+.IP
+<output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add
+the 'pairwise' modifier. To omit the main report, add the 'counts\-only'
+modifier. (Note that, if you're only interested in nonmissing autosomal
+biallelic hardcalls, \fB\-\-make\-king\-table\fR provides a more efficient way to
+compute just counts.)
+.IP
+* By default, if an output filename has a multipart sample ID, the parts
+.IP
+will be delimited by '_'; use 'fname\-id\-delim=' to change this.
+.IP
+Supported main\-report column sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(Variant ID is always present, and positioned here.)
+ref: Reference allele.
+alt: All alternate alleles, comma\-separated.
+maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
+fid: Force FID1/FID2 even when FID was absent in the input.
+id: IID1/IID2.
+maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
+sid: Force SID1/SID2 even when SID was absent in the input.
+geno: Unphased GT or DS for the two samples.
+.IP
+The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the
+sample IDs are removed from the default in 'pairwise' mode.
+Supported discordance\-count\-summary column sets are:
+.IP
+maybefid: FID1/FID2, if that column was in the input.
+fid: Force FID1/FID2 even when FID was absent in the input.
+(IID1/IID2 are always present.)
+maybesid: SID1/SID2, if that column was in the input.
+sid: Force SID1/SID2 even when SID was absent in the input.
+nobs: Number of variants considered. This includes variants where one or
+.IP
+both variants are missing iff 'include\-missing' was specified.
+.IP
+nobsibs: ibs0+ibs1+ibs2.
+ibs0: Number of diploid variants with no common hardcall alleles.
+ibs1: Number of diploid variants with exactly 1 common hardcall allele.
+ibs2: Number of diploid variants with both hardcall alleles matching.
+halfmiss: Number of variants with exactly 1 missing genotype/dosage.
+.IP
+Ignored without 'include\-missing'.
+.IP
+diff: Total number of differences.
+.IP
+The default is maybefid,maybesid,nobs,halfmiss,diff.
+.HP
+\fB\-\-make\-king\fR [{square | square0 | triangle}] [{zs | bin | bin4}]
+.IP
+KING\-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC,
+Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in
+genome\-wide association studies. By default, this writes a
+lower\-triangular tab\-delimited table of kinship coefficients to
+<output prefix>.king, and a list of the corresponding sample IDs to
+<output prefix>.king.id. The first row of the .king file contains a single
+<genome 1\-genome 2> kinship coefficient, the second row has the
+<genome 1\-genome 3> and <genome 2\-genome 3> kinship values in that order,
+etc.
+* Only autosomes are currently considered.
+* Pedigree information is currently ignored; the between\-family estimator
+.IP
+is used for all pairs.
+.IP
+* For multiallelic variants, REF allele counts are used.
+* 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 'zs' modifier is present, the .king file is Zstd\-compressed.
+* 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>.king.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
+* The computation can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-make\-king\-table\fR ['zs'] ['counts'] ['rel\-check'] ['cols='<col set descrip.>]
+.IP
+Similar to \fB\-\-make\-king\fR, except results are reported in KING's original
+\&.kin0 text table format (with minor changes, e.g. row order is more
+friendly to incremental addition of samples), \fB\-\-king\-table\-filter\fR can be
+used to restrict the report to high kinship values, and the 'rel\-check'
+modifier can be used to restrict to same\-FID pairs.
+Supported column sets are:
+.TP
+maybefid: FID1/FID2, if that column was in the input.
+Requires 'id'.
+.IP
+fid: Force FID1/FID2 even when FID was absent in the input.
+id: IID1/IID2.
+maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
+sid: Force SID1/SID2 even when SID was absent in the input.
+nsnp: Number of variants considered (autosomal, neither call missing).
+hethet: Proportion/count of considered call pairs which are het\-het.
+ibs0: Proportion/count of considered call pairs which are opposite homs.
+ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.
+kinship: KING\-robust between\-family kinship estimator.
+.IP
+The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.
+hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is
+present. If id is omitted, a .kin0.id file is also written.
+.HP
+\fB\-\-make\-rel\fR ['cov'] ['meanimpute'] [{square | square0 | triangle}]
+.IP
+[{zs | bin | bin4}]
+.IP
+Write a lower\-triangular variance\-standardized relationship matrix to
+<output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.
+* This computation assumes that variants do not have very low MAF, or
+.IP
+deviate greatly from Hardy\-Weinberg equilibrium.
+.IP
+* Also, it's usually best to perform this calculation on a variant set in
+.IP
+approximate linkage equilibrium.
+.IP
+* The 'cov' modifier replaces the variance\-standardization step with basic
+.IP
+mean\-centering, causing a covariance matrix to be calculated instead.
+.IP
+* The computation can be subdivided with \fB\-\-parallel\fR.
+.HP
+\fB\-\-make\-grm\-list\fR ['cov'] ['meanimpute'] ['zs'] [{id\-header | iid\-only}]
+.HP
+\fB\-\-make\-grm\-bin\fR ['cov'] ['meanimpute'] [{id\-header | iid\-only}]
+.HP
+\fB\-\-make\-grm\-list\fR causes the relationships to be written to GCTA's original
+.IP
+list 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.
+.HP
+\fB\-\-pca\fR [count] [{approx | meanimpute}] ['scols='<col set descriptor>]
+.HP
+\fB\-\-pca\fR [{allele\-wts | biallelic\-var\-wts}] [count] [{approx | meanimpute}]
+.IP
+['vzs'] ['scols='<col set descriptor>] ['vcols='<col set descriptor>]
+.IP
+Extracts top principal components from the variance\-standardized
+relationship matrix.
+* It is usually best to perform this calculation on a variant set in
+.IP
+approximate linkage equilibrium, with no very\-low\-MAF variants.
+.IP
+* By default, 10 PCs are extracted; you can adjust this by passing a
+.TP
+numeric argument.
+(Note that 10 is lower than the PLINK 1.9 default of
+.IP
+20; this is due to the randomized algorithm's memory footprint growing
+quadratically w.r.t. the PC count.)
+.IP
+* The 'approx' modifier causes the standard deterministic computation to be
+.IP
+replaced with the randomized algorithm originally implemented for
+Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,
+Price AL (2016) Fast Principal\-Component Analysis Reveals Convergent
+Evolution of ADH1B in Europe and East Asia. This can be a good idea when
+you have >5k samples, and is almost required with >50k.
+.IP
+* The randomized algorithm always uses mean imputation for missing genotype
+.TP
+calls.
+For comparison purposes, you can use the 'meanimpute' modifier to
+.IP
+request this behavior for the standard computation.
+.IP
+* 'scols=' can be used to customize how sample IDs appear in the .eigenvec
+.TP
+file.
+(maybefid, fid, maybesid, and sid supported; default is
+.IP
+maybefid,maybesid.)
+.IP
+* The 'allele\-wts' modifier requests an additional one\-line\-per\-allele
+.IP
+\&.eigenvec.allele file with PCs expressed as allele weights instead of
+sample weights. When it's present, 'vzs' causes the .eigenvec.allele
+file to be Zstd\-compressed.
+\&'vcols=' can be used to customize the report columns; supported column
+sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+(A1 is always present, and positioned here.)
+ax: Non\-A1 alleles, comma\-separated.
+(PCs are always present, and positioned here.)
+.IP
+Default is chrom,ref,alt.
+.IP
+* For datasets with no multiallelic variants, the 'biallelic\-var\-wts'
+.IP
+modifier requests the old .eigenvec.var format, which only reports
+weights for major alleles. (These weights are 2x the corresponding
+\&.eigenvec.allele weights.) Supported column sets are:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+maj: Major allele.
+nonmaj: Minor allele.
+(PCs are always present, and positioned here. Signs are w.r.t. the
+major, not necessarily reference, allele.)
+.IP
+Default is chrom,maj,nonmaj.
+.HP
+\fB\-\-king\-cutoff\fR [.king.bin + .king.id fileset prefix] <threshold>
+.IP
+Exclude one member of each pair of samples with KING\-robust kinship greater
+than the given threshold. Remaining/excluded sample IDs are written to
+<output prefix>.king.cutoff.in.id + .king.cutoff.out.id.
+If present, the .king.bin file must be triangular (either precision is ok).
+.HP
+\fB\-\-write\-covar\fR ['cols='<column set descriptor>]
+.IP
+If covariates are defined, an updated version (with all filters applied) is
+automatically written to <output prefix>.cov whenever \fB\-\-make\-pgen\fR,
+\fB\-\-make\-just\-psam\fR, \fB\-\-export\fR, or a similar command is present. However, if
+you do not wish to simultaneously generate a new sample file, you can use
+\fB\-\-write\-covar\fR to just produce a pruned covariate file.
+Supported column sets are:
+.IP
+maybefid: FID, if that column was in the input.
+fid: Force FID column to be written even when absent in the input.
+maybesid: SID, if that column was in the input.
+sid: Force SID column to be written even when absent in the input.
+maybeparents: Father/mother IIDs ('0' = missing), if columns in input.
+parents: Force PAT/MAT columns to be written even when absent in input.
+sex: '1' = male, '2' = female, 'NA' = missing.
+pheno1: First active phenotype. If none, all column entries are set to
+.IP
+the \fB\-\-output\-missing\-phenotype\fR string.
+.TP
+phenos: All active phenotypes, if any.
+(Can be combined with pheno1 to
+.IP
+force at least one phenotype column to be written.)
+.IP
+(Covariates are always present, and positioned here.)
+.IP
+The default is maybefid,maybesid.
+.HP
+\fB\-\-write\-samples\fR
+.IP
+Report IDs of all samples which pass your filters/inclusion thresholds.
+.HP
+\fB\-\-write\-snplist\fR ['zs'] ['allow\-dups']
+.TP
+List all variants which pass your filters/inclusion thresholds.
+Unless the
+.IP
+\&'allow\-dups' modifier is provided, this now errors out when duplicate
+variant ID(s) remain.
+.HP
+\fB\-\-glm\fR ['zs'] ['omit\-ref'] [{sex | no\-x\-sex}] ['log10'] ['pheno\-ids']
+.IP
+[{genotypic | hethom | dominant | recessive}] ['interaction'] ['skip']
+['hide\-covar'] [{no\-firth | firth\-fallback | firth}] ['intercept']
+['cols='<col set desc>] ['local\-covar='<file>] ['local\-psam='<file>]
+['local\-pos\-cols='<key col #s> | 'local\-pvar='<file>] ['local\-haps']
+['local\-omit\-last' | 'local\-cats[0]='<category ct>] ['allow\-no\-covars']
+.IP
+Basic association analysis on quantitative and/or case/control phenotypes.
+For each variant, a linear (for quantitative traits) or logistic (for
+case/control) regression is run with the phenotype as the dependent
+variable, and nonmajor allele dosage(s) and a constant\-1 column as
+predictors.
+* There is usually an additive effect line for every nonmajor allele, and
+.TP
+no such line for the major allele.
+To omit REF alleles instead of major
+.TP
+alleles, add the 'omit\-ref' modifier.
+(When performing interaction
+.IP
+testing, this tends to cause the multicollinearity check to fail for
+low\-ref\-frequency variants.)
+.IP
+* By default, sex (male = 1, female = 2; note that this is a change from
+.IP
+PLINK 1.x) is automatically added as a predictor for X chromosome
+variants, and no others. The 'sex' modifier causes it to be added
+everywhere (except chrY), while 'no\-x\-sex' excludes it entirely.
+.IP
+* The 'log10' modifier causes p\-values to be reported in \fB\-log10\fR(p) form.
+* 'pheno\-ids' causes the samples used in each set of regressions to be
+.TP
+written to an .id file.
+(When the samples differ on chrX or chrY, .x.id
+.IP
+and/or .y.id files are also written.)
+.IP
+* The 'genotypic' modifier adds an additive effect/dominance deviation 2df
+.IP
+joint test (0\-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and
+0..1..0 coding instead.
+.IP
+* 'dominant' and 'recessive' specify a model assuming full dominance or
+.TP
+recessiveness, respectively, for the ref allele.
+I.e. the genotype
+.IP
+column is recoded as 0..1..1 or 0..0..1, respectively.
+.TP
+* 'interaction' adds genotype x covariate interactions to the model.
+Note
+.IP
+that this tends to produce 'NA' results (due to the multicollinearity
+check) when the reference allele is 'wrong'; \fB\-\-maj\-ref\fR can be used to
+enable analysis of those variants.
+.TP
+* Additional predictors can be added with \fB\-\-covar\fR.
+By default, association
+.IP
+statistics are reported for all nonconstant predictors; 'hide\-covar'
+suppresses covariate\-only results, while 'intercept' causes intercepts
+to be reported.
+Since running \fB\-\-glm\fR without at least e.g. principal component covariates
+is usually an analytical mistake, the 'allow\-no\-covars' modifier is now
+required when you're intentionally running \fB\-\-glm\fR without a covariate
+file.
+.IP
+* By default, if the current phenotype and covariates are such that every
+.TP
+regression on a chromosome will fail, PLINK 2 errors out.
+To just skip
+.IP
+the phenotype or chromosome instead, add the 'skip' modifier.
+.IP
+* There are now three regression modes for case/control phenotypes:
+.IP
+* 'no\-firth' requests PLINK 1.x's behavior, where a NA result is reported
+.IP
+when basic logistic regression fails to converge.
+.IP
+* 'firth\-fallback' requests logistic regression, followed by Firth
+.TP
+regression whenever the logistic regression fails to converge.
+This is
+.IP
+now the default.
+.IP
+* 'firth' requests Firth regression all the time.
+.IP
+* To add covariates which are not constant across all variants, add the
+.IP
+\&'local\-covar=' and 'local\-psam=' modifiers, use full filenames for each,
+and use either 'local\-pvar=' or 'local\-pos\-cols=' to provide variant ID
+or position information.
+Normally, the local\-covar file should have c * n real\-valued columns,
+where the first c columns correspond to the first sample in the
+local\-psam file, columns (c+1) to 2c correspond to the second sample,
+etc.; and the mth line corresponds to the mth nonheader line of the
+local\-pvar file when there is one. (Variants outside of the local\-pvar
+file are excluded from the regression.) The local covariates are
+assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local
+covariate from the regression (necessary if they are e.g. local ancestry
+coefficients which sum to 1), add 'local\-omit\-last'.
+Alternatively, with 'local\-cats='<k>, the local\-covar file is expected to
+have n columns with integer\-valued entries in [1, k]. (This range is
+[0, k\-1] with 'local\-cats0='.) These category assignments are expanded
+into (k\-1) local covariates in the usual manner.
+When position information is in the local\-covar file, this should be
+indicated by 'local\-pos\-cols='<number of header rows>,<chrom col #>,<pos
+start col #>,<first covariate col #>.
+\&'local\-haps' indicates that there's one column or column\-group per
+haplotype instead of per sample; they are averaged by \fB\-\-glm\fR.
+.IP
+The main report supports the following column sets:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+(A1 is always present, and positioned here. For multiallelic variants,
+this column may contain multiple comma\-separated alleles when the result
+doesn't depend on which allele is A1.)
+ax: Non\-A1 alleles, comma\-separated.
+a1count: A1 allele count (can be decimal with dosage data).
+totallele: Allele observation count (can be higher than \fB\-\-freq\fR value, due
+.IP
+to inclusion of het haploids and chrX model).
+.IP
+a1countcc: A1 count in cases, then controls (case/control only).
+totallelecc: Case and control allele observation counts.
+gcountcc: Genotype hardcall counts (neither\-A1, het\-A1, A1\-A1) in cases,
+.IP
+then controls (case/control only).
+.IP
+a1freq: A1 allele frequency.
+a1freqcc: A1 frequency in cases, then controls (case/control only).
+machr2: Unphased MaCH imputation quality (frequently labeled 'INFO').
+firth: Reports whether Firth regression was used (firth\-fallback only).
+test: Test identifier. (Required unless only one test is run.)
+nobs: Number of samples in the regression.
+beta: Regression coefficient (for A1 if additive test).
+orbeta: Odds ratio for case/control, beta for quantitative traits.
+.IP
+(Ignored if 'beta' column set included.)
+.IP
+se: Standard error of beta.
+ci: Bounds of symmetric approximate confidence interval (requires \fB\-\-ci\fR).
+tz: T\-statistic for linear regression, Wald Z\-score for logistic/Firth..
+p: Asymptotic p\-value (or \fB\-log10\fR(p)) for T/Z\-statistic.
+err: Error code for NA results.
+.IP
+The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p,err.
+.HP
+\fB\-\-score\fR <filename> [i] [j] [k] [{header | header\-read}]
+.IP
+[{center | variance\-standardize | dominant | recessive}]
+['no\-mean\-imputation'] ['se'] ['zs'] ['ignore\-dup\-ids']
+[{list\-variants | list\-variants\-zs}] ['cols='<col set descriptor>]
+.IP
+Apply linear scoring system(s) to each sample.
+The input file should have one line per scored (variant, allele) pair.
+Variant IDs are read from column #i and allele codes are read from column
+#j, where i defaults to 1 and j defaults to i+1.
+* By default, a single column of input coefficients is read from column #k,
+.TP
+where k defaults to j+1.
+(\fB\-\-score\-col\-nums\fR can be used to specify
+.IP
+multiple columns.)
+.IP
+* 'header\-read' causes the first line of the input file to be treated as a
+.TP
+header line containing score names.
+Otherwise, score(s) are assigned the
+.IP
+names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line
+to be entirely ignored.
+.IP
+* By default, copies of unnamed alleles 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
+* You can use the 'center' modifier to shift all genotypes to mean zero, or
+.IP
+\&'variance\-standardize' to linearly transform the genotypes to mean\-0,
+variance\-1.
+.IP
+* The 'dominant' modifier causes dosages greater than 1 to be treated as 1,
+.IP
+while 'recessive' uses max(dosage \- 1, 0) on diploid chromosomes.
+('dominant', 'recessive', and 'variance\-standardize' cannot be used with
+chrX.)
+.IP
+* The 'se' modifier causes the input coefficients to be treated as
+.IP
+independent standard errors; in this case, standard errors for the score
+average/sum are reported. (Note that this will systematically
+underestimate standard errors when scored variants are in LD.)
+.IP
+* By default, \fB\-\-score\fR errors out if a variant ID in the input file appears
+.TP
+multiple times in the main dataset.
+Use the 'ignore\-dup\-ids' modifier to
+.IP
+skip them instead (a warning is still printed if such variants are
+present).
+.IP
+* The 'list\-variants[\-zs]' modifier causes variant IDs used for scoring to
+.IP
+be written to <output prefix>.sscore.vars[.zst].
+.IP
+The main report supports the following column sets:
+.IP
+maybefid: FID, if that column was in the input.
+fid: Force FID column to be written even when absent in the input.
+(IID is always present, and positioned here.)
+maybesid: SID, if that column was in the input.
+sid: Force SID column to be written even when absent in the input.
+pheno1: First active phenotype.
+phenos: All active phenotypes, if any.
+nallele: Number of nonmissing alleles.
+denom: Denominator of score average (equal to nallele value when
+.IP
+\&'no\-mean\-imputation' specified).
+.IP
+dosagesum: Sum of named allele dosages.
+scoreavgs: Score averages.
+scoresums: Score sums.
+.IP
+The default is maybefid,maybesid,phenos,nallele,dosagesum,scoreavgs.
+For more sophisticated polygenic risk scoring, we recommend looking at the
+LDpred (https://github.com/bvilhjal/ldpred ) and PRSice\-2
+(https://www.prsice.info/ ) software packages.
+.HP
+\fB\-\-variant\-score\fR <filename> ['zs'] ['bin' | 'cols='<col set descriptor>]
+.IP
+(alias: \fB\-\-vscore\fR)
+Apply linear scoring system(s) to each variant. Each reported variant
+score is the dot product of a sample\-weight vector with the
+total\-ALT\-dosage vector, with MAF\-based mean imputation applied to missing
+dosages.
+Input file format: one line per sample, each starting with an ID and
+followed by scoring weight(s); it can also have a header line with the
+sample ID representation and the score name(s).
+The usual .vscore text report supports the following column sets:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+altfreq: ALT allele frequency used for mean\-imputation.
+nmiss: Number of missing (and thus mean\-imputed) dosages.
+nobs: Number of (nonmissing) sample observations.
+(Variant scores are always present, and positioned here.)
+.IP
+Default is chrom,pos,ref,alt.
+If binary output is requested instead, the main .vscore.bin matrix contains
+double\-precision floating\-point values, column (score) ID(s) are saved to
+<output prefix>.vscore.cols, and variant IDs are saved to
+<output prefix>.vscore.vars[.zst].
+.HP
+\fB\-\-adjust\-file\fR <filename> ['zs'] ['gc'] ['cols='<column set descriptor>]
+.IP
+['log10'] ['input\-log10'] ['test='<test name, case\-sensitive>]
+.IP
+Given a file with unfiltered association test results, report some basic
+multiple\-testing corrections, sorted in increasing\-p\-value order.
+* 'gc' causes genomic\-controlled p\-values to be used in the formulas.
+.TP
+(This tends to be overly conservative.
+We note that LD Score regression
+.IP
+usually does a better job of calibrating lambda; see Lee JJ, McGue M,
+Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an
+estimator of confounding and genetic correlations in genome\-wide
+association studies.)
+.IP
+* 'log10' causes negative base 10 logs of p\-values to be reported, instead
+.TP
+of raw p\-values.
+\&'input\-log10' specifies that the input file contains
+.HP
+\fB\-log10\fR(p) values.
+.IP
+* If the input file contains multiple tests per variant which are
+.IP
+distinguished by a 'TEST' column (true for \fB\-\-linear\fR/\-\-logistic/\-\-glm),
+you must use 'test=' to select the test to process.
+.IP
+The following column sets are supported:
+.IP
+chrom: Chromosome ID.
+pos: Base\-pair coordinate.
+(ID is always present, and positioned here.)
+ref: Reference allele.
+alt1: Alternate allele 1.
+alt: All alternate alleles, comma\-separated.
+a1: Tested allele. (Omitted if missing from input file.)
+unadj: Unadjusted p\-value.
+gc: Devlin & Roeder (1999) genomic control corrected p\-value (additive
+.IP
+models only).
+.IP
+qq: P\-value quantile.
+bonf: Bonferroni correction.
+holm: Holm\-Bonferroni (1979) adjusted p\-value.
+sidakss: Sidak single\-step adjusted p\-value.
+sidaksd: Sidak step\-down adjusted p\-value.
+fdrbh: Benjamini & Hochberg (1995) step\-up false discovery control.
+fdrby: Benjamini & Yekutieli (2001) step\-up false discovery control.
+.IP
+Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby.
+.HP
+\fB\-\-genotyping\-rate\fR ['dosage']
+.IP
+Report genotyping rate in log (this was automatic in PLINK 1.x).
+.HP
+\fB\-\-pgen\-info\fR
+.IP
+Reports basic information about a .pgen file.
+.HP
+\fB\-\-validate\fR
+.IP
+Validates all variant records in a .pgen file.
+.HP
+\fB\-\-zst\-decompress\fR <.zst file> [output filename]
+.IP
+(alias: \fB\-\-zd\fR)
+Decompress a Zstd\-compressed file. If no output filename is specified, the
+file is decompressed to standard output.
+This cannot be used with any other flags, and does not cause a log file to
+be generated.
+.PP
+The following other flags are supported.
+.TP
+\fB\-\-script\fR <fname>
+: Include command\-line options from file.
+.TP
+\fB\-\-rerun\fR [log]
+: Rerun commands in log (default 'plink2.log').
+.TP
+\fB\-\-version\fR
+: Display only version number before exiting.
+.TP
+\fB\-\-silent\fR
+: Suppress regular output to console. (Error\-output is
+not suppressed.)
+.TP
+\fB\-\-double\-id\fR
+: Set both FIDs and IIDs to the VCF/.bgen sample ID.
+.TP
+\fB\-\-const\-fid\fR [ID]
+: Set all FIDs to the given constant. If '0' (the
+default), no FID column is created.
+.TP
+\fB\-\-id\-delim\fR [d]
+: Normally parses single\-delimiter sample IDs as
+<FID><d><IID>, and double\-delimiter IDs as
+<FID><d><IID><d><SID>; default delimiter is '_'.
+\fB\-\-id\-delim\fR can no longer be used with
+\fB\-\-double\-id\fR/\-\-const\-fid; it will error out if any ID
+lacks the delimiter.
+.TP
+\fB\-\-idspace\-to\fR <c>
+: Convert spaces in VCF/.bgen sample IDs to the given
+character.
+.TP
+\fB\-\-iid\-sid\fR
+: Make \fB\-\-id\-delim\fR and \fB\-\-sample\-diff\fR interpret two\-token
+sample IDs as IID\-SID instead of FID\-IID.
+.TP
+\fB\-\-vcf\-require\-gt\fR
+: Skip variants with no GT field.
+.TP
+\fB\-\-vcf\-min\-gq\fR <val>
+: No\-call genotypes when GQ is present and below the
+threshold.
+.TP
+\fB\-\-vcf\-max\-dp\fR <val>
+: No\-call genotypes when DP is present and above/below
+.TP
+\fB\-\-vcf\-min\-dp\fR <val>
+the 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 name>
+: Specify single\-chromosome .gen/.bgen file
+with no useful chromosome info inside.
+.TP
+\fB\-\-missing\-code\fR [string list]
+: Comma\-delimited list of missing phenotype
+.TP
+(alias: \fB\-\-missing_code\fR)
+values for Oxford\-format import (default
+\&'NA').
+.TP
+\fB\-\-hard\-call\-threshold\fR <val>
+: When importing dosage data, a hardcall is
+normally saved when the distance from the
+nearest hardcall, defined as
+.TP
+0.5 * sum_i |x_i \- round(x_i)|
+(where the x_i's are 0..2 allele dosages),
+is not greater than 0.1. You can adjust
+this threshold by providing a numeric
+argument to \fB\-\-hard\-call\-threshold\fR.
+You can also use this with \fB\-\-make\-[b]pgen\fR
+to alter the saved hardcalls while leaving
+the dosages untouched, or \fB\-\-make\-bed\fR to
+tweak hardcall export.
+.TP
+\fB\-\-dosage\-erase\-threshold\fR <val>
+: \fB\-\-hard\-call\-threshold\fR normally preserves
+the original dosages, and several PLINK 2
+commands use them when they're available.
+Use \fB\-\-dosage\-erase\-threshold\fR to make PLINK
+2 erase dosages and keep only hardcalls
+when distance\-from\-hardcall <= the given
+level.
+.TP
+\fB\-\-import\-dosage\-certainty\fR <val> : The PLINK 2 file format currently supports
+a single dosage for each allele. Some
+other dosage file formats include a
+separate probability for every possible
+genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52,
+P(1/1)=0.28}, a highly uncertain call that
+is nevertheless treated as a hardcall under
+\&'\-\-hard\-call\-threshold 0.1'. To make PLINK
+2 treat a dosage as missing whenever the
+largest probability is less than a
+threshold, use \fB\-\-import\-dosage\-certainty\fR.
+.TP
+\fB\-\-input\-missing\-genotype\fR <c> : '.' is always interpreted as a missing
+genotype code in input files. By default, '0'
+also is; you can change this second missing
+code with \fB\-\-input\-missing\-genotype\fR.
+.TP
+\fB\-\-allow\-extra\-chr\fR
+: Permit unrecognized chromosome codes (alias \fB\-\-aec\fR).
+.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 <val>
+: Alias for '\-\-chr\-set <value> no\-y no\-xy no\-mt'.
+.TP
+\fB\-\-human\fR
+: Explicitly specify human chromosome set, and make
+output .pvar/VCF files include a ##chrSet header
+line. (.pvar/VCF output files automatically
+include ##chrSet when a nonhuman set is specified.)
+.TP
+\fB\-\-chr\-override\fR ['file'] : By default, if \fB\-\-chr\-set\fR/\-\-autosome\-num/\-\-cow/etc.
+conflicts with an input file ##chrSet header line,
+PLINK 2 will error out. \fB\-\-chr\-override\fR with no
+argument causes the command line to take
+precedence; '\-\-chr\-override file' defers to the
+file.
+.TP
+\fB\-\-var\-min\-qual\fR <val>
+: Skip variants with low/missing QUAL.
+.TP
+\fB\-\-var\-filter\fR [exception(s)...]
+: Skip variants which have FILTER failures.
+.HP
+\fB\-\-extract\-if\-info\fR <key> <op> <val> : Exclude variants which don't/do satisfy
+.TP
+\fB\-\-exclude\-if\-info\fR <key> <op> <val>
+a comparison predicate on an INFO key,
+.TP
+(aliases: \fB\-\-extract\-if\fR,
+e.g.
+.TP
+\fB\-\-exclude\-if\fR)
+\fB\-\-extract\-if\-info\fR "VT == SNP"
+.TP
+Unless the operator is !=, the predicate
+always evaluates to false when the key
+is missing.
+.TP
+\fB\-\-require\-info\fR <key(s)...>
+: Exclude variants based on nonexistence
+.TP
+\fB\-\-require\-no\-info\fR <key(s)...>
+or existence of an INFO key. "<key>=."
+is treated as nonexistence.
+.HP
+\fB\-\-extract\-col\-cond\fR <f> [valcol] [IDcol] [skip] :
+.HP
+\fB\-\-extract\-col\-cond\-match\fR <(sub)string(s)...>
+.HP
+\fB\-\-extract\-col\-cond\-mismatch\fR <(sub)string(s)...>
+.HP
+\fB\-\-extract\-col\-cond\-substr\fR
+.HP
+\fB\-\-extract\-col\-cond\-min\fR <min>
+.HP
+\fB\-\-extract\-col\-cond\-max\fR <max> :
+.IP
+Exclude all variants without a value\-column entry satisfying a condition.
+* By default, values are read from column 2 of the file, and variant IDs
+.IP
+are read from column 1.
+.IP
+* Three types of conditions are supported:
+.IP
+* When \fB\-\-extract\-col\-cond\-match\fR is specified without
+.HP
+\fB\-\-extract\-col\-cond\-substr\fR, the value is checked for equality with the
+.TP
+given strings, and kept iff one of them matches.
+Similarly,
+.HP
+\fB\-\-extract\-col\-cond\-mismatch\fR without \fB\-\-extract\-col\-cond\-substr\fR causes
+.IP
+the variant to be kept iff the value matches none of the given strings.
+.IP
+* When \fB\-\-extract\-col\-cond\-match\fR and/or \fB\-mismatch\fR are specified with
+.HP
+\fB\-\-extract\-col\-cond\-substr\fR, the variant is kept iff none of the
+.HP
+\fB\-\-extract\-col\-cond\-mismatch\fR substrings are contained in the value, and
+.IP
+either \fB\-\-extract\-col\-cond\-match\fR was unspecified or at least one of its
+substrings is contained.
+.IP
+* Otherwise, the value is interpreted as a number, and the variant is
+.IP
+kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX)..
+.TP
+\fB\-\-pheno\fR ['iid\-only'] <f> : Specify additional phenotype/covariate file.
+Comma\-delimited files with a header line are now
+permitted.
+.TP
+\fB\-\-pheno\-name\fR <name...>
+: Only load the designated phenotype(s) from the
+\fB\-\-pheno\fR (if one was specified) or .psam (if no
+\fB\-\-pheno\fR) file. Separate multiple names with
+spaces or commas, and use dashes to designate
+ranges.
+.TP
+\fB\-\-pheno\-col\-nums\fR <#...>
+: Only load the phenotype(s) in the designated
+column number(s) from the \fB\-\-pheno\fR file.
+.TP
+\fB\-\-no\-psam\-pheno\fR
+: Ignore phenotype(s) in .psam/.fam file.
+.TP
+\fB\-\-strict\-sid0\fR
+: By default, if there is no SID column in the .psam/.fam
+(or \fB\-\-update\-ids\fR) file, but there is one in another
+input file (for e.g. \fB\-\-keep\fR/\-\-remove), the latter SID
+column is ignored; sample IDs are considered matching as
+long as FID and IID are equal (with missing FID treated
+as '0'). If you also want to require SID = '0' for a
+sample ID match in this situation, add \fB\-\-strict\-sid0\fR.
+.TP
+\fB\-\-input\-missing\-phenotype\fR <v> : Set nonzero number to treat as a missing
+pheno/covar in input files (default \fB\-9\fR).
+.TP
+\fB\-\-no\-input\-missing\-phenotype\fR
+: Don't treat any nonzero number as a missing
+pheno/covar. ('NA'/'nan' are still treated
+as missing.)
+.TP
+\fB\-\-1\fR
+: Expect case/control phenotypes in input files
+to be coded as 0 = control, 1 = case, instead
+of the usual 0 = missing, 1 = ctrl, 2 = case.
+(Unlike PLINK 1.x, this does not force all
+phenotypes to be interpreted as case/ctrl.)
+.TP
+\fB\-\-missing\-catname\fR <str>
+: Set missing\-categorical\-phenotype string
+(case\-sensitive, default 'NONE').
+.TP
+\fB\-\-covar\fR ['iid\-only'] <f> : Specify additional covariate file.
+Comma\-delimited files with a header line are now
+permitted.
+.TP
+\fB\-\-covar\-name\fR <name...>
+: Only load the designated covariate(s) from the
+\fB\-\-covar\fR (if one was specified), \fB\-\-pheno\fR (if no
+\fB\-\-covar\fR), or .psam (if no \fB\-\-covar\fR or \fB\-\-pheno\fR)
+file.
+.TP
+\fB\-\-covar\-col\-nums\fR <#...>
+: Only load the covariate(s) in the designated
+column number(s) from the \fB\-\-covar\fR (if one was
+specified) or \fB\-\-pheno\fR (if no \fB\-\-covar\fR) file.
+.TP
+\fB\-\-within\fR <f> [new pheno name] : Import a PLINK 1.x categorical phenotype.
+(Phenotype name defaults to 'CATPHENO'.)
+* If any numeric values are present, ALL
+.TP
+values must be numeric.
+In that case, 'C'
+.TP
+is added in front of all category names.
+* 'NA' is treated as a missing value.
+.TP
+\fB\-\-mwithin\fR <n>
+: Load \fB\-\-within\fR categories from column n+2.
+.TP
+\fB\-\-family\fR [new pheno name]
+: Create a categorical phenotype from FID.
+Restrictions on and handling of numeric
+values are the same as for \fB\-\-within\fR.
+.TP
+\fB\-\-family\-missing\-catname\fR <nm> : Make \fB\-\-family\fR treat the specified FID as
+missing.
+.TP
+\fB\-\-keep\fR <fname...>
+: Exclude all samples not named in a file.
+.TP
+\fB\-\-remove\fR <fname...>
+: Exclude all samples named in a file.
+.TP
+\fB\-\-keep\-fam\fR <fn...>
+: Exclude all families not named in a file.
+.TP
+\fB\-\-remove\-fam\fR <f...>
+: Exclude all families named in a file.
+.HP
+\fB\-\-extract\fR [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named
+.TP
+\fB\-\-exclude\fR [{bed0 | bed1}] <f...>
+in the given file(s). When multiple files
+are named, they are concatenated.
+With the 'bed0' or 'bed1' modifier,
+variants outside/inside the positional
+ranges in the interval\-BED file(s) are
+excluded instead. 'bed0' tells PLINK 2 to
+assume the interval bounds follow the UCSC
+0\-based half\-open convention, while 'bed1'
+(equivalent to PLINK 1.9 'range')
+specifies 1\-based fully\-closed.
+.TP
+\fB\-\-extract\-intersect\fR [{bed0 | bed1}] <f...> : Just like \fB\-\-extract\fR, except that
+a variant must be in the
+intersection, rather than just
+the union, of the files to
+remain.
+.TP
+\fB\-\-bed\-border\-bp\fR <n>
+: Stretch BED intervals by the given amount on each
+.TP
+\fB\-\-bed\-border\-kb\fR <n>
+side.
+.TP
+\fB\-\-keep\-cats\fR <filename>
+: These can be used individually or in combination
+.TP
+\fB\-\-keep\-cat\-names\fR <nm...>
+to define a list of categories to keep; all
+samples not in one of the named categories are
+excluded. Use spaces to separate category names
+for \fB\-\-keep\-cat\-names\fR. Use the \fB\-\-missing\-catname\fR
+value (default 'NONE') to refer to the group of
+uncategorized samples.
+.TP
+\fB\-\-keep\-cat\-pheno\fR <pheno> : If more than one categorical phenotype is loaded,
+or you wish to filter on a categorical covariate,
+\fB\-\-keep\-cat\-pheno\fR must be used to specify which
+phenotype/covariate \fB\-\-keep\-cats\fR and
+\fB\-\-keep\-cat\-names\fR apply to.
+.HP
+\fB\-\-remove\-cats\fR <filename> : Exclude all categories named in the file.
+.HP
+\fB\-\-remove\-cat\-names\fR <...> : Exclude named categories.
+.HP
+\fB\-\-remove\-cat\-pheno\fR <phe> : Specify pheno for \fB\-\-remove\-cats\fR/remove\-cat\-names.
+.TP
+\fB\-\-split\-cat\-pheno\fR [{omit\-most | omit\-last}] ['covar\-01']
+[cat. pheno/covar name(s)...] :
+.IP
+Split n\-category phenotype(s) into n (or n\-1, with 'omit\-most'/'omit\-last')
+binary phenotypes, with names of the form <orig. pheno name>=<cat. name>.
+(As a consequence, affected phenotypes and categories are not permitted to
+contain the '=' character.)
+* This happens after all sample filters.
+* If no phenotype or covariate names are provided, all categorical
+.IP
+phenotypes (but not covariates) are processed.
+.TP
+* By default, generated covariates are coded as 1=false, 2=true.
+To code
+.IP
+them as 0=false, 1=true instead, add the 'covar\-01' modifier.
+.TP
+\fB\-\-loop\-cats\fR <pheno/covar>
+: Run variant filters and subsequent operations
+on just the samples in the first category; then
+just the samples in the second category; and so
+on, for all categories in the named categorical
+phenotype.
+.TP
+\fB\-\-no\-id\-header\fR ['iid\-only'] : Don't include a header line in .id output
+files. This normally forces two\-column FID/IID
+output; add 'iid\-only' to force just
+single\-column IID.
+.HP
+\fB\-\-variance\-standardize\fR [pheno/covar name(s)...]
+.HP
+\fB\-\-covar\-variance\-standardize\fR [covar name(s)...] :
+.IP
+Linearly transform named covariates (and quantitative phenotypes, if
+\fB\-\-variance\-standardize\fR) to mean\-zero, variance 1. If no arguments are
+provided, all possible phenotypes/covariates are affected.
+This is frequently necessary to prevent multicollinearity when dealing with
+covariates where abs(mean) is much larger than abs(standard deviation),
+such as year of birth.
+.TP
+\fB\-\-quantile\-normalize\fR [...]
+: Force named covariates and quantitative
+.TP
+\fB\-\-pheno\-quantile\-normalize\fR [...]
+phenotypes to a N(0,1) distribution,
+.TP
+\fB\-\-covar\-quantile\-normalize\fR [...]
+preserving only the original rank orders.
+.TP
+\fB\-\-chr\fR <chr(s)...>
+: Exclude all variants not on the given chromosome(s).
+Valid choices for humans are 0 (unplaced), 1\-22, X, Y,
+XY, MT, PAR1, and PAR2. 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, par1, x, par2'.
+.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\-par\fR
+: Exclude all non\-autosomal variants, except those in a
+pseudo\-autosomal region.
+.TP
+\fB\-\-snps\-only\fR ['just\-acgt'] : Exclude non\-SNP variants.
+By default, SNP = all
+allele codes are single\-character (so
+multiallelic variants with a mix of SNPs and
+non\-SNPs are excluded; split your variants first
+if that's a problem).
+The 'just\-acgt' modifier restricts SNP 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.
+(\fB\-\-snps\fR can be used to specify intervals which cross
+chromosome boundaries.)
+.TP
+\fB\-\-snp\fR
+<var ID> : Specify a single variant to load.
+.HP
+\fB\-\-exclude\-snp\fR <ID> : Specify a single variant to exclude.
+.TP
+\fB\-\-window\fR
+<kbs> : With \fB\-\-snp\fR/\-\-exclude\-snp, loads/excludes all variants
+within half the specified kb distance of the named one.
+.TP
+\fB\-\-from\-bp\fR <pos>
+: Use base\-pair coordinates to define a variant range to
+.TP
+\fB\-\-to\-bp\fR
+<pos> load.
+.TP
+\fB\-\-from\-kb\fR <pos>
+* You must use these with \fB\-\-chr\fR, specifying a single
+.TP
+\fB\-\-to\-kb\fR
+<pos> chromosome.
+.TP
+\fB\-\-from\-mb\fR <pos>
+* Decimals and negative numbers are permitted.
+.TP
+\fB\-\-to\-mb\fR
+<pos> * The \fB\-\-to\-bp\fR(/\-kb/\-mb) position is no longer permitted
+to be smaller than the \fB\-\-from\-bp\fR position.
+.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\-\-force\-intersect\fR
+: PLINK 2 normally errors out when multiple variant
+inclusion filters (\fB\-\-extract\fR, \fB\-\-extract\-col\-cond\fR,
+\fB\-\-extract\-intersect\fR, \fB\-\-from\fR/\-\-to, \fB\-\-from\-bp\fR/\-\-to\-bp,
+\fB\-\-snp\fR, \fB\-\-snps\fR) are specified. \fB\-\-force\-intersect\fR
+allows the run to proceed; the set intersection will
+be taken.
+.TP
+\fB\-\-thin\fR <p>
+: Randomly remove variants, retaining each with prob. p.
+.TP
+\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.
+.TP
+\fB\-\-thin\-indiv\fR <p>
+: Randomly remove samples, retaining with prob. p.
+.HP
+\fB\-\-thin\-indiv\-count\fR <n> : Randomly remove samples until n of them remain.
+.TP
+\fB\-\-keep\-col\-match\fR <f> <val(s)...> : Exclude all samples without a 3rd column
+entry in the given file exactly matching
+one of the given strings. (Separate
+multiple strings with spaces.)
+.HP
+\fB\-\-keep\-col\-match\-name\fR <col name> : Check column with given name instead.
+.TP
+\fB\-\-keep\-col\-match\-num\fR <n>
+: Check nth column instead.
+.HP
+\fB\-\-geno\fR [val] [{dosage | hh\-missing}]
+.HP
+\fB\-\-mind\fR [val] [{dosage | hh\-missing}] :
+.IP
+Exclude variants (\fB\-\-geno\fR) and/or samples (\fB\-\-mind\fR) with missing call
+frequencies greater than a threshold (default 0.1). (Note that the default
+threshold is only applied if \fB\-\-geno\fR/\-\-mind is invoked without an argument;
+when \fB\-\-geno\fR/\-\-mind is not invoked, no missing call frequency ceiling is
+enforced at all. Other inclusion/exclusion default thresholds work the
+same way.)
+By default, when a dosage is present but a hardcall is not, the genotype is
+treated as missing; add the 'dosage' modifier to treat this case as
+nonmissing. Alternatively, you can use 'hh\-missing' to also treat
+heterozygous haploid calls as missing.
+.HP
+\fB\-\-require\-pheno\fR [name(s)...] : Remove samples missing any of the named
+.TP
+\fB\-\-require\-covar\fR [name(s)...]
+phenotype(s)/covariate(s). If no arguments
+are provided, all phenotype(s)/covariate(s)
+must be present.
+.TP
+\fB\-\-maf\fR [freq] [mode]
+: Exclude variants with allele frequency lower than a
+.TP
+(alias: \fB\-\-min\-af\fR)
+threshold (default 0.01). By default, the nonmajor
+allele frequency is used; the other supported modes
+are 'nref' (non\-reference), 'alt1', and 'minor'
+(least frequent). bcftools freq:mode notation is
+permitted.
+.HP
+\fB\-\-max\-maf\fR <freq> [mode] : Exclude variants with MAF greater than the
+.TP
+(alias: \fB\-\-max\-af\fR)
+threshold.
+.TP
+\fB\-\-mac\fR <ct> [mode]
+: Exclude variants with allele dosage lower than the
+.TP
+(alias: \fB\-\-min\-ac\fR)
+given threshold.
+.TP
+\fB\-\-max\-mac\fR <ct> [mode]
+: Exclude variants with allele dosage greater than
+.TP
+(alias: \fB\-\-max\-ac\fR)
+the given threshold.
+.TP
+\fB\-\-maf\-succ\fR
+: Rule of succession allele frequency estimation (used in
+EIGENSOFT). Given j observations of one allele and k
+observations of the other for a biallelic variant, infer
+allele frequencies of (j+1) / (j+k+2) and
+(k+1) / (j+k+2), rather than the default j / (j+k) and
+k / (j+k).
+Note that this does not affect \fB\-\-freq\fR's output.
+.TP
+\fB\-\-min\-alleles\fR <ct> : Exclude variants with fewer than the given # of alleles.
+(When a variant has exactly one ALT allele, and it's
+a missing\-code, it's excluded by "\-\-min\-alleles 2".)
+.HP
+\fB\-\-max\-alleles\fR <ct> : Exclude variants with more than the given # of alleles.
+.TP
+\fB\-\-read\-freq\fR <file> : Load allele frequency estimates from the given \fB\-\-freq\fR or
+\fB\-\-geno\-counts\fR (or PLINK 1.9 \fB\-\-freqx\fR) report, instead of
+imputing them from the immediate dataset.
+.HP
+\fB\-\-hwe\fR <p> ['midp'] ['keep\-fewhet'] :
+.IP
+Exclude variants with Hardy\-Weinberg equilibrium exact test p\-values below
+a threshold.
+* By default, only founders are considered.
+* chrX p\-values are now computed using Graffelman and Weir's method.
+* For variants with k alleles with k>2, k separate 'biallelic' tests are
+.IP
+performed, and the variant is filtered out if any of them fail.
+.IP
+* With 'keep\-fewhet', variants which fail the test in the too\-few\-hets
+.TP
+direction are not excluded.
+On chrX, this uses the ratio between the
+.IP
+Graffelman/Weir p\-value and the female\-only p\-value.
+.IP
+* There is currently no special handling of case/control phenotypes.
+.TP
+\fB\-\-mach\-r2\-filter\fR [min] [max] : Exclude variants with MaCH imputation quality
+metric less than min or greater than max
+(defaults 0.1 and 2.0). (Monomorphic
+variants, with r2 = nan, are not excluded.)
+* This is NOT identical to the R2 metric
+.TP
+reported by Minimac3 0.1.13+; see below.
+* If a single argument is provided, it is
+.TP
+treated as the minimum.
+* The metric is not computed on chrX and MT.
+.TP
+\fB\-\-minimac3\-r2\-filter\fR <min> [max] : Compute Minimac3 R2 values from scratch,
+and exclude variants with R2 less than min
+or (if max is provided) greater than max.
+* Note that this requires phased\-dosage
+.TP
+data for all samples and variants;
+otherwise this will systematically
+underestimate imputation quality, since
+unphased hardcalls/dosages are treated
+as if they were maximally uncertain.
+(Use \fB\-\-extract\-if\-info\fR/\-\-exclude\-if\-info
+to filter on precomputed Minimac3 R2 in
+a VCF/.pvar INFO column.)
+.TP
+\fB\-\-keep\-females\fR
+: Exclude male and unknown\-sex samples.
+.TP
+\fB\-\-keep\-males\fR
+: Exclude female and unknown\-sex samples.
+.TP
+\fB\-\-keep\-nosex\fR
+: Exclude all known\-sex samples.
+.TP
+\fB\-\-remove\-females\fR
+: Exclude female samples.
+.TP
+\fB\-\-remove\-males\fR
+: Exclude male samples.
+.TP
+\fB\-\-remove\-nosex\fR
+: Exclude unknown\-sex samples.
+.TP
+\fB\-\-keep\-founders\fR
+: Exclude nonfounder samples.
+.HP
+\fB\-\-keep\-nonfounders\fR : Exclude founder samples.
+.HP
+\fB\-\-keep\-if\fR <pheno/covar> <op> <val> : Exclude samples which don't/do satisfy a
+.TP
+\fB\-\-remove\-if\fR <pheno/covar> <op> <v>
+comparison predicate, e.g.
+\fB\-\-keep\-if\fR "PHENO1 == case"
+.TP
+Unless the operator is !=, the predicate
+always evaluates to false when the
+phenotype/covariate is missing.
+.TP
+\fB\-\-nonfounders\fR
+: Include nonfounders in allele freq/HWE calculations.
+.TP
+\fB\-\-bad\-freqs\fR
+: When PLINK 2 needs decent allele frequencies, it
+normally errors out if they aren't provided by
+\fB\-\-read\-freq\fR and less than 50 founders are available to
+impute them from. Use \fB\-\-bad\-freqs\fR to force PLINK 2 to
+proceed in this case.
+.TP
+\fB\-\-bad\-ld\fR
+: PLINK 2 normally errors out when it needs to estimate LD
+between variants, but there are less than 50 founders to
+estimate from. Use \fB\-\-bad\-ld\fR to force PLINK 2 to
+proceed.
+.TP
+\fB\-\-export\-allele\fR <file> : With \fB\-\-export\fR A/A\-transpose/AD, count alleles named
+in the file, instead of REF alleles.
+.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'; default is now 'MT' (note that this is
+a change from PLINK 1.x, which defaulted to '26').
+.TP
+\fB\-\-output\-missing\-genotype\fR <ch> : Set the code used to represent missing
+genotypes in output files (default '.').
+.TP
+\fB\-\-output\-missing\-phenotype\fR <s> : Set the string used to represent missing
+phenotypes in output files (default 'NA').
+.TP
+\fB\-\-sort\-vars\fR [mode]
+: Sort variants by chromosome, then position, then
+ID. The following string orders are supported:
+* 'natural'/'n': Natural sort (default).
+* 'ascii'/'a': ASCII.
+This must be used with \fB\-\-make\-[b]pgen\fR/\-\-make\-bed.
+.TP
+\fB\-\-set\-hh\-missing\fR ['keep\-dosage'] : Make \fB\-\-make\-[b]pgen\fR/\-\-make\-bed set non\-MT
+heterozygous haploid hardcalls, and all
+female chrY calls, to missing. (Unlike
+PLINK 1.x, this treats unknown\-sex chrY
+genotypes like males, not females.)
+By default, all associated dosages are
+also erased; use 'keep\-dosage' to keep
+them all.
+.TP
+\fB\-\-set\-mixed\-mt\-missing\fR ['keep\-dosage'] : Make \fB\-\-make\-[b]pgen\fR/\-\-make\-bed set
+mixed MT hardcalls to missing.
+.HP
+\fB\-\-split\-par\fR <bp1> <bp2> : Changes chromosome code of all X chromosome
+.TP
+\fB\-\-split\-par\fR <build>
+variants with bp position <= bp1 to PAR1, and those
+with position >= bp2 to PAR2. The following build
+codes are supported as shorthand:
+* 'b36'/'hg18' = NCBI 36, 2709521/154584237
+* 'b37'/'hg19' = GRCh37, 2699520/154931044
+* 'b38'/'hg38' = GRCh38, 2781479/155701383
+.TP
+\fB\-\-merge\-par\fR
+: Merge PAR1/PAR2 back with X. Requires PAR1 to be
+positioned immediately before X, and PAR2 to be
+immediately after X. (Should *not* be used with
+"\-\-export vcf", since it causes male
+homozygous/missing calls in PAR1/PAR2 to be
+reported as haploid.)
+.TP
+\fB\-\-merge\-x\fR
+: Merge XY back with X. This usually has to be
+combined with \fB\-\-sort\-vars\fR.
+.TP
+\fB\-\-set\-missing\-var\-ids\fR <t>
+: Given a template string with a '@' where the
+.TP
+\fB\-\-set\-all\-var\-ids\fR <t>
+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, while \fB\-\-set\-all\-var\-ids\fR resets all
+IDs.
+You may also use '$r'/'$a' to refer to the
+ref and alt1 alleles, or '$1'/'$2' to refer to
+them in alphabetical order.
+.TP
+\fB\-\-var\-id\-multi\fR <t>
+: Specify alternative templates for multiallelic
+.TP
+\fB\-\-var\-id\-multi\-nonsnp\fR <t>
+variants. ('$a' and '$1'/'$2' should be avoided
+here, though they're technically still allowed.)
+.HP
+\fB\-\-new\-id\-max\-allele\-len\fR <len> [{error | missing | truncate}] :
+.IP
+Specify maximum number of leading characters from allele codes to include
+in new variant IDs, and behavior on longer codes (defaults 23, error).
+.TP
+\fB\-\-missing\-var\-code\fR <str>
+: Change unnamed variant code for \fB\-\-rm\-dup\fR,
+\fB\-\-set\-\fR{missing|all}\-var\-ids, and
+\fB\-\-recover\-var\-ids\fR (default '.').
+.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\-\-recover\-var\-ids\fR <file> ['strict\-bim\-order'] [{rigid | force}] ['partial'] :
+.TP
+Undo \fB\-\-set\-all\-var\-ids\fR, given the original .pvar/VCF/.bim file.
+Original
+.IP
+IDs are looked up by position and allele codes.
+* By default, if the original\-ID file is a .bim, allele order is ignored.
+.IP
+Use 'strict\-bim\-order' to force A1=ALT, A2=REF.
+.IP
+* If any variant has multiple matching records in the original\-ID file, and
+.IP
+the IDs conflict, \fB\-\-recover\-var\-ids\fR writes the affected (current) ID(s)
+to <output prefix>.recoverid.dup, and normally errors out. If the
+original\-ID file has the same number of variants in the same order, you
+can still recover the old IDs with the 'rigid' modifier in this case.
+Alternatively, to proceed and assign the missing\-ID code to these
+variants, add the 'force' modifier. (The .recoverid.dup file is still
+written when 'rigid' or 'force' is specified.)
+.IP
+* \fB\-\-recover\-var\-ids\fR normally expects to replace all variant IDs, and errors
+.TP
+out if any are left untouched.
+Add the 'partial' modifier when you
+.IP
+actually want to update just a proper subset.
+.TP
+\fB\-\-update\-alleles\fR <fname>
+: Update variant allele codes.
+.TP
+\fB\-\-update\-ids\fR <fname>
+: Update sample IDs.
+.TP
+\fB\-\-update\-parents\fR <fname>
+: Update parental IDs.
+.HP
+\fB\-\-update\-sex\fR <filename> ['col\-num='<n>] ['male0'] :
+.IP
+Update sex information.
+* By default, if there is a header line starting with '#FID'/'#IID', sex is
+.IP
+loaded from the first column titled 'SEX' (any capitalization);
+otherwise, column 3 is assumed. Use 'col\-num=' to force a column number.
+.TP
+* Only the first character in the sex column is processed.
+By default,
+.IP
+\&'1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,
+and '0'/'N' is interpreted as unknown\-sex. To change this to '0'/'M'/'m'
+= male, '1'/'F'/'f' = female, anything else other than '2' = unknown\-sex,
+add 'male0'.
+.TP
+\fB\-\-real\-ref\-alleles\fR
+: Treat A2 alleles in a PLINK 1.x fileset as actual REF
+alleles; otherwise they're marked as provisional.
+.TP
+\fB\-\-maj\-ref\fR ['force'] : Set major alleles to reference, like PLINK 1.x
+automatically did. (Note that this is now opt\-in
+rather than opt\-out; \fB\-\-keep\-allele\-order\fR is no longer
+necessary to prevent allele\-swapping.)
+* This can only be used in runs with
+.TP
+\fB\-\-make\-bed\fR/\-\-make\-[b]pgen/\-\-export and no other
+commands.
+.TP
+* By default, this only affects variants marked as
+having 'provisional' reference alleles. Add 'force'
+to apply this to all variants.
+.IP
+* All new reference alleles are marked as provisional.
+.HP
+\fB\-\-ref\-allele\fR ['force'] <filename> [refcol] [IDcol] [skip]
+.HP
+\fB\-\-alt1\-allele\fR ['force'] <filename> [alt1col] [IDcol] [skip] :
+.IP
+These set the alleles specified in the file to ref (\fB\-\-ref\-allele\fR) or alt1
+(\fB\-\-alt1\-allele\fR). They can be combined in the same run.
+* These can only be used in runs with \fB\-\-make\-bed\fR/\-\-make\-[b]pgen/\-\-export
+.IP
+and no other commands.
+.IP
+* "\-\-ref\-allele <VCF filename> 4 3 '#'", which scrapes reference allele
+.IP
+assignments from a VCF file, is especially useful.
+.IP
+* By default, these error out when asked to change a 'known' reference
+.TP
+allele.
+Add 'force' to permit that (when e.g. switching to a new
+.IP
+reference genome).
+.IP
+* When \fB\-\-alt1\-allele\fR changes the previous ref allele to alt1, the previous
+.IP
+alt1 allele is set to reference and marked as provisional.
+.TP
+\fB\-\-ref\-from\-fa\fR ['force'] : This sets reference alleles from the \fB\-\-fa\fR file when
+it can be done unambiguously (note that it's never
+possible for deletions or some insertions).
+By default, it errors out when asked to change a
+\&'known' reference allele; add the 'force' modifier
+to permit that.
+.TP
+\fB\-\-normalize\fR ['list']
+: Left\-normalize all variants, using the \fB\-\-fa\fR file.
+.TP
+(alias: \fB\-\-norm\fR)
+(Assumes no differences in capitalization.) The
+\&'list' modifier causes a list of affected variant
+IDs to be written to <output prefix>.normalized.
+.TP
+\fB\-\-indiv\-sort\fR <mode> [f] : Specify sample ID sort order for merge and
+\fB\-\-make\-[b]pgen\fR/\-\-make\-bed. The following four
+modes are supported:
+* 'none'/'0' keeps samples in the order they were
+.TP
+loaded.
+Default for non\-merge.
+.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 last argument).
+.TP
+\fB\-\-king\-table\-filter\fR <min>
+: Specify minimum kinship coefficient for
+inclusion in \fB\-\-make\-king\-table\fR report.
+.TP
+\fB\-\-king\-table\-subset\fR <f> [kmin] : Restrict current \fB\-\-make\-king\-table\fR run to
+sample pairs listed in the given .kin0 file.
+If a second argument is provided, only
+sample pairs with kinship >= that threshold
+(in the input .kin0) are processed.
+.HP
+\fB\-\-condition\fR <variant ID> [{dominant | recessive}] ['multiallelic']
+.HP
+\fB\-\-condition\-list\fR <fname> [{dominant | recessive}] ['multiallelic'] :
+.IP
+Add the given variant, or all variants in the given file, as \fB\-\-glm\fR
+covariates.
+By default, this errors out if any of the variants are multiallelic; add
+the 'multiallelic' ('m' for short) modifier to allow them. They'll
+effectively be split against the major allele (unless \fB\-\-glm\fR's 'omit\-ref'
+modifier was specified), and all induced covariate names\-\-even for
+biallelic variants\-\-will have an underscore followed by the allele code at
+the end.
+.TP
+\fB\-\-parameters\fR <...> : Include only the given covariates/interactions in the
+\fB\-\-glm\fR model, identified by a list of 1\-based indices
+and/or ranges of them.
+.TP
+\fB\-\-tests\fR <...>
+: Perform a (joint) test on the specified term(s) in the
+.TP
+\fB\-\-tests\fR all \fB\-\-glm\fR model, identified by 1\-based indices and/or ranges
+of them.
+* 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\-\-glm\fR multicollinearity check
+(default 50). (This is no longer skipped for
+case/control phenotypes.)
+.TP
+\fB\-\-max\-corr\fR <val>
+: Skip \fB\-\-glm\fR regression when the absolute value of the
+correlation between two predictors exceeds this value
+(default 0.999).
+.TP
+\fB\-\-xchr\-model\fR <m>
+: Set the chrX \fB\-\-glm\fR/\-\-condition[\-list]/\-\-[v]score model.
+* '0' = skip chrX.
+* '1' = add sex as a covar on chrX, code males 0..1.
+* '2' (default) = chrX sex covar, code males 0..2.
+(Use the \fB\-\-glm\fR 'interaction' modifier to test for
+interaction between genotype and sex.)
+.HP
+\fB\-\-adjust\fR ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] :
+.IP
+For each association test in this run, report some basic multiple\-testing
+corrections, sorted in increasing\-p\-value order. Modifiers work the same
+way as they do on \fB\-\-adjust\-file\fR.
+.TP
+\fB\-\-lambda\fR
+: Set genomic control lambda for \fB\-\-adjust[\-file]\fR.
+.TP
+\fB\-\-adjust\-chr\-field\fR <n...>
+: Set \fB\-\-adjust\-file\fR input field names. When
+.TP
+\fB\-\-adjust\-pos\-field\fR <n...>
+multiple arguments are given to these flags,
+.TP
+\fB\-\-adjust\-id\-field\fR <n...>
+earlier names take precedence over later ones.
+.HP
+\fB\-\-adjust\-ref\-field\fR <n...>
+.HP
+\fB\-\-adjust\-alt\-field\fR <n...>
+.HP
+\fB\-\-adjust\-a1\-field\fR <n...>
+.HP
+\fB\-\-adjust\-test\-field\fR <n...>
+.HP
+\fB\-\-adjust\-p\-field\fR <n...>
+.TP
+\fB\-\-ci\fR <size>
+: Report confidence ratios for odds ratios/betas.
+.TP
+\fB\-\-pfilter\fR <val>
+: Filter out assoc. test results with higher p\-values.
+.TP
+\fB\-\-score\-col\-nums\fR <...> : Process all the specified coefficient columns in the
+\fB\-\-score\fR file, identified by 1\-based indexes and/or
+ranges of them.
+.HP
+\fB\-\-q\-score\-range\fR <range file> <data file> [i] [j] ['header'] ['min'] :
+.IP
+Apply \fB\-\-score\fR to subset(s) of variants in the primary score list(s) 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 line
+.TP
+(except possibly the first).
+Variant IDs are read from column #i and
+.IP
+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.
+.IP
+* By default, \fB\-\-q\-score\-range\fR errors out when a variant ID appears multiple
+.TP
+times in the data file (and is also present in the main dataset).
+To use
+.IP
+the minimum p\-value in this case instead, add the 'min' modifier.
+.TP
+\fB\-\-vscore\-col\-nums\fR <...> : Process all the specified coefficient columns in
+the \fB\-\-variant\-score\fR file, identified by 1\-based
+indexes and/or ranges of them.
+.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. plink2.king.13
+or plink2.king.13.zst if k is 13. Concatenating these
+files in order will yield the full matrix of interest.
+(Yes, this can be done before decompression.)
+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> ['require'] : Set size, in MiB, of initial workspace malloc
+attempt. To error out instead of reducing the
+request size when the initial attempt fails, add
+the 'require' modifier.
+.TP
+\fB\-\-threads\fR <val>
+: Set maximum number of compute threads.
+.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.
+Note that \fB\-\-threads\fR and "\-\-memory require" may also be
+needed to reproduce some randomized runs.
+.TP
+\fB\-\-output\-min\-p\fR <p> : Specify minimum p\-value to write to reports.
+(2.23e\-308
+is useful for preventing underflow in some programs.)
+.TP
+\fB\-\-debug\fR
+: Use slower, more crash\-resistant logging method.
+.TP
+\fB\-\-randmem\fR
+: Randomize initial workspace memory (helps catch
+uninitialized\-memory bugs).
+.TP
+\fB\-\-warning\-errcode\fR
+: Return a nonzero error code to the OS when a run
+completes with warning(s).
+.TP
+\fB\-\-zst\-level\fR <lvl>
+: Set the Zstd compression level (1\-22, default 3).
+.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.
+.SH "SEE ALSO"
+The full documentation for
+.B PLINK v2.00a3 64-bit (9 Apr
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B PLINK v2.00a3 64-bit (9 Apr
+programs are properly installed at your site, the command
+.IP
+.B info PLINK v2.00a3 64-bit (9 Apr
+.PP
+should give you access to the complete manual.
=====================================
debian/rules
=====================================
@@ -14,11 +14,13 @@ override_dh_auto_clean:
override_dh_auto_build:
dh_auto_build
- help2man --no-discard-stderr --name="whole genome SNP analysis" $(DIRECTORY)/plink2 > plink2.1
+# help2man 1.47.13 is not able anymore do generate a clean manpage for plink1.9
+# which lead to several lintian warnings
+# help2man --no-discard-stderr --name="whole genome SNP analysis" $(DIRECTORY)/plink2 > plink2.1
help2man --no-discard-stderr --name="whole genome SNP analysis" $(DIRECTORY)/pgen_compress > pgen_compress.1
override_dh_installman:
- dh_installman plink2.1
+ dh_installman debian/plink2.1
dh_installman pgen_compress.1
override_dh_installchangelogs:
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/7f9b980e5aefd8fa948ab9571a95ce7ebc1c4bc5...01274352f062d9c7b637cba5d737dcefc3d23012
--
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/7f9b980e5aefd8fa948ab9571a95ce7ebc1c4bc5...01274352f062d9c7b637cba5d737dcefc3d23012
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200421/dfef79d8/attachment-0001.html>
More information about the debian-med-commit
mailing list