This is an automated email from the git hooks/post-receive script. bob.dybian-guest pushed a commit to branch master in repository plink1.9.
commit 93e9bf7452f8517a7d30c6465d5da310b3a434b7 Author: Dylan Aïssi <[email protected]> Date: Fri Jan 23 06:34:14 2015 +0100 Refresh d/* --- debian/control | 5 +- debian/copyright | 30 + debian/manpages | 2 +- debian/patches/01_Fix_use_internal_lib.patch | 10 +- debian/patches/02_Activate_Hardening.patch | 6 +- debian/patches/03_Rename_binary_to_plink1.9.patch | 6 +- debian/patches/04_Activate_Stable_Build.patch | 2 +- debian/plink1.9.1 | 2242 --------------------- debian/rules | 4 + debian/tests/output_tests/{README.out => README} | 4 +- debian/tests/run-sample-analysis | 6 +- 11 files changed, 55 insertions(+), 2262 deletions(-) diff --git a/debian/control b/debian/control index aa5a322..68ee2c6 100644 --- a/debian/control +++ b/debian/control @@ -4,6 +4,7 @@ Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Dylan Aïssi <[email protected]> Build-Depends: debhelper (>= 9.0.0), + help2man, libatlas-base-dev, liblapack-dev, zlib1g-dev @@ -26,8 +27,8 @@ Description: whole-genome association analysis toolset disease phenotypes. The joint investigation of copy number variations is supported. A variety of statistical tests have been implemented. . - plink1.9 is a comprehensive update of plink with new algorithms and new methods, - faster and less memory consumer than the first plink. + plink1.9 is a comprehensive update of plink with new algorithms and new + methods, faster and less memory consumer than the first plink. . Please note: The executable was renamed to plink1.9 because of a name clash. Please read more about this diff --git a/debian/copyright b/debian/copyright index e963feb..2c15498 100644 --- a/debian/copyright +++ b/debian/copyright @@ -12,6 +12,18 @@ Files: pigz.c Copyright: 2007-2013 Mark Adler, Christopher Chang License: Zlib +Files: Rconnection.cc +Copyright: 2004-8 Simon Urbanek +License: LGPL-2.1 + +Files: Rsrv.h +Copyright: 2002-13 Simon Urbanek +License: LGPL-2.1 + +Files: sisocks.h +Copyright: 2000,1 Simon Urbanek +License: LGPL-2.1 + Files: SFMT.* Copyright: 2006-2012 Mutsuo Saito, Makoto Matsumoto, Hiroshima University and The University of Tokyo License: BSD-3-clause @@ -75,6 +87,24 @@ License: Zlib misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. +License: LGPL-2.1 + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation; version 2.1 of the License + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Leser General Public License for more details. + . + You should have received a copy of the GNU Lesser General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. + . + Although this code is licensed under LGPL v2.1, we strongly encourage + everyone modifying this software to contribute back any improvements and + bugfixes to the project for the benefit all other users. Thank you. + License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/debian/manpages b/debian/manpages index 0f65186..f7e585b 100644 --- a/debian/manpages +++ b/debian/manpages @@ -1 +1 @@ -debian/*.1 +*.1 diff --git a/debian/patches/01_Fix_use_internal_lib.patch b/debian/patches/01_Fix_use_internal_lib.patch index 021b476..56070a5 100644 --- a/debian/patches/01_Fix_use_internal_lib.patch +++ b/debian/patches/01_Fix_use_internal_lib.patch @@ -1,6 +1,6 @@ Author: Dylan Aïssi <[email protected]> Description: Fix the use of Debian internal libraries. -Last-Update: 2014-11-25 +Last-Update: 2015-01-23 Forwarded: No --- a/Makefile @@ -10,16 +10,16 @@ Forwarded: No CFLAGS=-Wall -O2 -BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas --LINKFLAGS=-lm -lpthread +-LINKFLAGS=-lm -lpthread -ldl -ZLIB=zlib-1.2.8/libz.so.1.2.8 +BLASFLAGS=-llapack -lcblas -latlas -+LINKFLAGS=-lm -lpthread -lz ++LINKFLAGS=-lm -lpthread -ldl -lz +#ZLIB=zlib-1.2.8/libz.so.1.2.8 ifeq ($(SYS), MAC) GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300) -@@ -55,8 +55,9 @@ - # either renaming that binary to "plink1" or this one to "plink2". +@@ -57,8 +57,9 @@ + # lead to minor problems when PLINK 2.0 is released.) plink: $(SRC) - g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) diff --git a/debian/patches/02_Activate_Hardening.patch b/debian/patches/02_Activate_Hardening.patch index a6c29ce..d7627ed 100644 --- a/debian/patches/02_Activate_Hardening.patch +++ b/debian/patches/02_Activate_Hardening.patch @@ -1,12 +1,12 @@ Author: Dylan Aïssi <[email protected]> Description: Activate Hardening FLAGs. -Last-Update: 2014-11-25 +Last-Update: 2015-01-23 Forwarded: No --- a/Makefile +++ b/Makefile -@@ -55,9 +55,9 @@ - # either renaming that binary to "plink1" or this one to "plink2". +@@ -57,9 +57,9 @@ + # lead to minor problems when PLINK 2.0 is released.) plink: $(SRC) - g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) diff --git a/debian/patches/03_Rename_binary_to_plink1.9.patch b/debian/patches/03_Rename_binary_to_plink1.9.patch index a196013..d5f184e 100644 --- a/debian/patches/03_Rename_binary_to_plink1.9.patch +++ b/debian/patches/03_Rename_binary_to_plink1.9.patch @@ -1,12 +1,12 @@ Author: Dylan Aïssi <[email protected]> Description: Rename binary from plink to plink1.9 to avoid name conflict with the first plink and the plink from ssh clone putty. -Last-Update: 2014-12-22 +Last-Update: 2015-01-23 Forwarded: https://github.com/chrchang/plink-ng/issues/12 --- a/Makefile +++ b/Makefile -@@ -55,9 +55,9 @@ - # either renaming that binary to "plink1" or this one to "plink2". +@@ -57,9 +57,9 @@ + # lead to minor problems when PLINK 2.0 is released.) plink: $(SRC) - g++ $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) diff --git a/debian/patches/04_Activate_Stable_Build.patch b/debian/patches/04_Activate_Stable_Build.patch index 4f2aed9..3968e78 100644 --- a/debian/patches/04_Activate_Stable_Build.patch +++ b/debian/patches/04_Activate_Stable_Build.patch @@ -1,6 +1,6 @@ Author: Dylan Aïssi <[email protected]> Description: Activate stable build. -Last-Update: 2014-12-22 +Last-Update: 2015-01-23 Forwarded: No --- a/plink_common.h diff --git a/debian/plink1.9.1 b/debian/plink1.9.1 deleted file mode 100644 index da99d76..0000000 --- a/debian/plink1.9.1 +++ /dev/null @@ -1,2242 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10. -.TH PLINK "1" "December 2014" "PLINK v1.90b2t 64-bit (20 Dec 2014)" "User Commands" -.SH NAME -PLINK2 \- manual page for PLINK v1.90b2t 64-bit (20 Dec 2014) -.SH DESCRIPTION -PLINK v1.90b2t 64\-bit (20 Dec 2014) https://www.cog\-genomics.org/plink2 -(C) 2005\-2014 Shaun Purcell, Christopher Chang GNU General Public License v3 -.PP -In the command line flag definitions that follow, -.IP -* [square brackets] denote a required parameter, where the text between the -.IP -brackets describes its nature. -.IP -* <angle brackets> denote an optional modifier (or if '|' is present, a set -.TP -of mutually exclusive optional modifiers). -Use the EXACT text in the -.IP -definition, e.g. '\-\-dummy acgt'. -.IP -* There's one exception to the angle brackets/exact text rule: when an angle -.IP -bracket term ends with '=[value]', '[value]' designates a variable -parameter. -.IP -* {curly braces} denote an optional parameter, where the text between the -.IP -braces describes its nature. -.IP -* An ellipsis (...) indicates that you may enter multiple parameters of the -.IP -specified type. -.IP -plink [input flag(s)...] {command flag(s)...} {other flag(s)...} -plink \fB\-\-help\fR {flag name(s)...} -.PP -Most PLINK runs require exactly one main input fileset. The following flags -are available for defining its form and location: -.HP -\fB\-\-bfile\fR {prefix} : Specify .bed + .bim + .fam prefix (default 'plink'). -.HP -\fB\-\-bed\fR [filename] : Specify full name of .bed file. -.HP -\fB\-\-bim\fR [filename] : Specify full name of .bim file. -.HP -\fB\-\-fam\fR [filename] : Specify full name of .fam file. -.TP -\fB\-\-keep\-autoconv\fR -: With \fB\-\-file\fR/\-\-tfile/\-\-lfile/\-\-vcf/\-\-bcf/\-\-data/\-\-23file, -don't delete autogenerated binary fileset at end of run. -.TP -\fB\-\-file\fR {prefix} -: Specify .ped + .map filename prefix (default 'plink'). -.HP -\fB\-\-ped\fR [filename] : Specify full name of .ped file. -.HP -\fB\-\-map\fR [filename] : Specify full name of .map file. -.TP -\fB\-\-no\-fid\fR -: .fam/.ped file does not contain column 1 (family ID). -.TP -\fB\-\-no\-parents\fR -: .fam/.ped file does not contain columns 3\-4 (parents). -.TP -\fB\-\-no\-sex\fR -: .fam/.ped file does not contain column 5 (sex). -.TP -\fB\-\-no\-pheno\fR -: .fam/.ped file does not contain column 6 (phenotype). -.HP -\fB\-\-tfile\fR {prefix} : Specify .tped + .tfam filename prefix (default 'plink'). -.TP -\fB\-\-tped\fR [fname] -: Specify full name of .tped file. -.TP -\fB\-\-tfam\fR [fname] -: Specify full name of .tfam file. -.HP -\fB\-\-lfile\fR {prefix} : Specify .lgen + .map + .fam (long\-format fileset) prefix. -.HP -\fB\-\-reference\fR [fn] : Specify default allele file accompanying \fB\-\-lfile\fR input. -.TP -\fB\-\-allele\-count\fR -: When used with \fB\-\-lfile\fR + \fB\-\-reference\fR, specifies that the -\&.lgen file contains reference allele counts. -.HP -\fB\-\-vcf\fR [filename] : Specify full name of .vcf or .vcf.gz file. -.HP -\fB\-\-bcf\fR [filename] : Specify full name of BCF2 file. -.TP -\fB\-\-data\fR {prefix} -: Specify Oxford .gen + .sample prefix (default 'plink'). -.HP -\fB\-\-gen\fR [filename] : Specify full name of .gen or .gen.gz file. -.HP -\fB\-\-bgen\fR [f] <snpid\-chr> : Specify full name of .bgen file. -.HP -\fB\-\-sample\fR [fname] : Specify full name of .sample file. -.HP -\fB\-\-23file\fR [fname] {FID} {IID} {sex} {pheno} {pat. ID} {mat. ID} : -.IP -Specify 23andMe input file. -.TP -\fB\-\-grm\-gz\fR {prfx} -: Specify .grm.gz + .grm.id (GCTA rel. matrix) prefix. -.TP -\fB\-\-grm\-bin\fR {prfx} : Specify .grm.bin + .grm.N.bin + .grm.id (GCTA triangular -binary relationship matrix) filename prefix. -.HP -\fB\-\-dummy\fR [sample ct] [SNP ct] {missing geno freq} {missing pheno freq} -.IP -<acgt | 1234 | 12> <scalar\-pheno> -.IP -This generates a fake input dataset with the specified number of samples -and SNPs. By default, the missing genotype and phenotype frequencies are -zero, and genotypes are As and Bs (change the latter with -\&'acgt'/'1234'/'12'). The 'scalar\-pheno' modifier causes a normally -distributed scalar phenotype to be generated instead of a binary one. -.HP -\fB\-\-simulate\fR [simulation parameter file] <tags | haps> <acgt | 1234 | 12> -.HP -\fB\-\-simulate\-qt\fR [simulation parameter file] <tags | haps> <acgt | 1234 | 12> -.HP -\fB\-\-simulate\fR generates a fake input dataset with disease\-associated SNPs, -.IP -while \fB\-\-simulate\-qt\fR generates a dataset with quantitative trait loci. -.PP -Output files have names of the form 'plink.{extension}' by default. You can -change the 'plink' prefix with -.TP -\fB\-\-out\fR [prefix] -: Specify prefix for output files. -.PP -Most runs also require at least one of the following commands: -.HP -\fB\-\-make\-bed\fR -.TP -Create a new binary fileset. -Unlike the automatic text\-to\-binary -.IP -converters (which only heed chromosome filters), this supports all of -PLINK's filtering flags. -.HP -\fB\-\-make\-just\-bim\fR -.HP -\fB\-\-make\-just\-fam\fR -.TP -Variants of \fB\-\-make\-bed\fR which only write a new .bim or .fam file. -Can be -.IP -used with only .bim/.fam input. -USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary -genotype data and your .bim/.fam indexes if you use these commands -improperly. If you have any doubt, stick with \fB\-\-make\-bed\fR. -.HP -\fB\-\-recode\fR <01 | 12> <23 | A{\-transpose} | AD | beagle{\-nomap} | bimbam{\-1chr} -.IP -| compound\-genotypes | fastphase{\-1chr} | HV{\-1chr} | lgen{\-ref} | -list | oxford | rlist | structure | transpose | vcf | vcf\-fid | -vcf\-iid> <tab | tabx | spacex> <include\-alt> -.TP -Create a new text fileset with all filters applied. -By default, the -.IP -fileset consists of a .ped and a .map file, readable with \fB\-\-file\fR. -* The '12' modifier causes A1 (usually minor) alleles to be coded as '1' -.IP -and A2 alleles to be coded as '2', while '01' maps A1 \-> 0 and A2 \-> 1. -.TP -* The '23' modifier causes a 23andMe\-formatted file to be generated. -This -.IP -can only be used on a single sample's data (\fB\-\-keep\fR may be handy). -.IP -* The 'AD' modifier causes an sample\-major additive (0/1/2) + dominant -.IP -(het = 1, otherwise 0) component file, suitable for loading from R, to be -generated. If you don't want the dominant component, use 'A' instead. -If you need uncounted alleles to be named in the header line, add the -\&'include\-alt' modifier. -.IP -* The 'A\-transpose' modifier causes a variant\-major additive component file -.IP -to be generated. -.IP -* The 'beagle' modifier causes unphased per\-autosome .dat and .map files, -.IP -readable by early BEAGLE versions, to be generated, while 'beagle\-nomap' -generates a single .beagle.dat file. -.IP -* The 'bimbam' modifier causes a BIMBAM\-formatted fileset to be generated. -.IP -If your input data only contains one chromosome, you can use -\&'bimbam\-1chr' instead to write a two\-column .pos.txt file. -.IP -* The 'compound\-genotypes' modifier removes the space between pairs of -.IP -allele codes for the same variant when generating a .ped + .map fileset. -.IP -* The 'fastphase' modifier causes per\-chromosome fastPHASE files to be -.TP -generated. -If your input data only contains one chromosome, you can use -.IP -\&'fastphase\-1chr' instead to exclude the chromosome number from the file -extension. -.IP -* The 'HV' modifier causes a Haploview\-format .ped + .info fileset to be -.TP -generated per chromosome. -\&'HV\-1chr' is analogous to 'fastphase\-1chr'. -.IP -* The 'lgen' modifier causes a long\-format fileset (loadable with \fB\-\-lfile\fR) -.IP -to be generated, while 'lgen\-ref' generates a (usually) smaller -long\-format fileset loadable with \fB\-\-lfile\fR + \fB\-\-reference\fR. -.IP -* The 'list' modifier creates a genotype\-based list, while 'rlist' creates -.IP -a rare\-genotype fileset. -.IP -* 'oxford' causes an Oxford\-format .gen + .sample fileset to be generated. -* The 'structure' modifier causes a Structure\-format file to be generated. -* 'transpose' creates a transposed text fileset (loadable with \fB\-\-tfile\fR). -* 'vcf', 'vcf\-fid', and 'vcf\-iid' result in production of a VCFv4.1 file. -.IP -\&'vcf\-fid' and 'vcf\-iid' cause family IDs or within\-family IDs -respectively to be used for the sample IDs in the last header row, while -\&'vcf' merges both IDs and puts an underscore between them. The A2 allele -is saved as the reference; when it is important for reference alleles to -be correct, you'll usually also want to include \fB\-\-a2\-allele\fR in your -command. -.IP -* The 'tab' modifier makes the output mostly tab\-delimited instead of -.TP -mostly space\-delimited. -\&'tabx' and 'spacex' force all tabs and all -.IP -spaces, respectively. -.HP -\fB\-\-flip\-scan\fR <verbose> -.IP -(alias: \fB\-\-flipscan\fR) -LD\-based scan for case/control strand inconsistency. -.HP -\fB\-\-write\-covar\fR -.IP -If a \fB\-\-covar\fR file is loaded, \fB\-\-make\-bed\fR/\-\-make\-just\-fam and \fB\-\-recode\fR -automatically generate an updated version (with all filters applied). -However, if you do not wish to simultaneously generate a new genotype file, -you can use \fB\-\-write\-covar\fR to just produce a pruned covariate file. -.HP -\fB\-\-write\-cluster\fR <omit\-unassigned> -.IP -If clusters are specified with \fB\-\-within\fR/\-\-family, this generates a new -cluster file (with all filters applied). The 'omit\-unassigned' modifier -causes unclustered samples to be omitted from the file; otherwise their -cluster is 'NA'. -.HP -\fB\-\-write\-set\fR -.HP -\fB\-\-set\-table\fR -.IP -If sets have been defined, \fB\-\-write\-set\fR dumps 'END'\-terminated set -membership lists to {output prefix}.set, while \fB\-\-set\-table\fR writes a -variant\-by\-set membership table to {output prefix}.set.table. -.HP -\fB\-\-merge\fR [.ped filename] [.map filename] -.HP -\fB\-\-merge\fR [text fileset prefix] -.HP -\fB\-\-bmerge\fR [.bed filename] [.bim filename] [.fam filename] -.HP -\fB\-\-bmerge\fR [binary fileset prefix] -.IP -Merge the given fileset with the initially loaded fileset, writing the -result to {output prefix}.bed + .bim + .fam. (It is no longer necessary to -simultaneously specify \fB\-\-make\-bed\fR.) -.HP -\fB\-\-merge\-list\fR [filename] -.IP -Merge all filesets named in the text file with the reference fileset, if -one was specified. (However, this can also be used *without* a reference; -in that case, the newly created fileset is then treated as the reference by -most other PLINK operations.) The text file is interpreted as follows: -* If a line contains only one name, it is assumed to be the prefix for a -.IP -binary fileset. -.IP -* If a line contains exactly two names, they are assumed to be the full -.IP -filenames for a text fileset (.ped first, then .map). -.IP -* If a line contains exactly three names, they are assumed to be the full -.IP -filenames for a binary fileset (.bed, then .bim, then .fam). -.HP -\fB\-\-write\-snplist\fR -.HP -\fB\-\-list\-23\-indels\fR -.HP -\fB\-\-write\-snplist\fR writes a .snplist file listing the names of all variants -.IP -which pass the filters and inclusion thresholds you've specified, while -\fB\-\-list\-23\-indels\fR writes the subset with 23andMe\-style indel calls (D/I -allele codes). -.HP -\fB\-\-freq\fR <counts> -.HP -\fB\-\-freqx\fR -.HP -\fB\-\-freq\fR generates a basic allele frequency (or count, if the 'counts' -.TP -modifier is present) report. -This can be combined with \fB\-\-within\fR/\-\-family -.IP -to produce a cluster\-stratified allele frequency/count report instead. -\fB\-\-freqx\fR generates a more detailed genotype count report, designed for use -with \fB\-\-read\-freq\fR. -.HP -\fB\-\-missing\fR -.TP -Generate sample\- and variant\-based missing data reports. -If clusters are -.IP -defined, the variant\-based report is cluster\-stratified. -.HP -\fB\-\-test\-mishap\fR -.IP -Check for association between missing calls and flanking haplotypes. -.HP -\fB\-\-hardy\fR <midp> -.TP -Generate a Hardy\-Weinberg exact test p\-value report. -(This does NOT -.TP -simultaneously filter on the p\-value any more; use \fB\-\-hwe\fR for that.) -With -.IP -the 'midp' modifier, the test applies the mid\-p adjustment described in -Graffelman J, Moreno V (2013) The mid p\-value in exact tests for -Hardy\-Weinberg Equilibrium. -.HP -\fB\-\-mendel\fR -.IP -Generate a Mendel error report. -.HP -\fB\-\-het\fR <small\-sample> -.HP -\fB\-\-ibc\fR -.TP -Estimate inbreeding coefficients. -\fB\-\-het\fR reports method\-of\-moments -.IP -estimates, while \fB\-\-ibc\fR calculates all three values described in Yang J, Lee -SH, Goddard ME and Visscher PM (2011) GCTA: A Tool for Genome\-wide Complex -Trait Analysis. (That paper also describes the relationship matrix -computation we reimplement.) -* These functions require decent MAF estimates. If there are very few -.IP -samples in your immediate fileset, \fB\-\-read\-freq\fR is practically mandatory -since imputed MAFs are wildly inaccurate in that case. -.IP -* They also assume the marker set is in approximate linkage equilibrium. -* By default, \fB\-\-het\fR omits the n/(n\-1) multiplier in Nei's expected -.TP -homozygosity formula. -The 'small\-sample' modifier causes it to be -.IP -included, while forcing \fB\-\-het\fR to use MAFs imputed from founders in the -immediate dataset. -.HP -\fB\-\-check\-sex\fR {female max F} {male min F} -.TP -\fB\-\-check\-sex\fR ycount {female max F} {male min F} {female max Y obs} -{male min Y obs} -.HP -\fB\-\-check\-sex\fR y\-only {female max Y obs} {male min Y obs} -.HP -\fB\-\-impute\-sex\fR {female max F} {male min F} -.TP -\fB\-\-impute\-sex\fR ycount {female max F} {male min F} {female max Y obs} -{male min Y obs} -.HP -\fB\-\-impute\-sex\fR y\-only {female max Y obs} {male min Y obs} -.HP -\fB\-\-check\-sex\fR normally compares sex assignments in the input dataset with -.IP -those imputed from X chromosome inbreeding coefficients. -* Make sure that the X chromosome pseudo\-autosomal region has been split -.IP -off (with e.g. \fB\-\-split\-x\fR) before using this. -.IP -* You also need decent MAF estimates (so, with very few samples in your -.IP -immediate fileset, use \fB\-\-read\-freq\fR), and your marker set should be in -approximate linkage equilibrium. -.IP -* By default, F estimates smaller than 0.2 yield female calls, and values -.TP -larger than 0.8 yield male calls. -If you pass numeric parameter(s) to -.HP -\fB\-\-check\-sex\fR, the first two control these thresholds. -.IP -There are now two modes which consider Y chromosome data. -* In 'ycount' mode, gender is still imputed from the X chromosome, but -.IP -female calls are downgraded to ambiguous whenever more than 0 nonmissing -Y genotypes are present, and male calls are downgraded when fewer than 0 -are present. (Note that these are counts, not rates.) These thresholds -are controllable with \fB\-\-check\-sex\fR ycount's optional 3rd and 4th numeric -parameters. -.IP -* In 'y\-only' mode, gender is imputed from nonmissing Y genotype counts. -.IP -The male minimum threshold defaults to 1 instead of zero in this case. -.HP -\fB\-\-impute\-sex\fR changes sex assignments to the imputed values, and is -.TP -otherwise identical to \fB\-\-check\-sex\fR. -It must be used with -.HP -\fB\-\-make\-bed\fR/\-\-recode/\-\-write\-covar. -.HP -\fB\-\-fst\fR <case\-control> -.IP -(alias: \fB\-\-Fst\fR) -Estimate Wright's Fst for each autosomal diploid variant using the method -introduced in Weir BS, Cockerham CC (1984) Estimating F\-statistics for the -analysis of population structure, given a set of subpopulations defined via -\fB\-\-within\fR. Raw and weighted global means are also reported. -* If you're interested in the global means, it is usually best to perform -.IP -this calculation on a marker set in approximate linkage equilibrium. -.IP -* If you have only two subpopulations, you can represent them with -.IP -case/control status and use the 'case\-control' modifier. -.HP -\fB\-\-indep\fR [window size]<kb> [step size (variant ct)] [VIF threshold] -.HP -\fB\-\-indep\-pairwise\fR [window size]<kb> [step size (variant ct)] [r^2 threshold] -.HP -\fB\-\-indep\-pairphase\fR [window size]<kb> [step size (variant ct)] [r^2 threshold] -.TP -Generate a list of markers in approximate linkage equilibrium. -With the -.IP -\&'kb' modifier, the window size is in kilobase instead of variant count -units. (Pre\-'kb' space is optional, i.e. '\-\-indep\-pairwise 500 kb 5 0.5' -and '\-\-indep\-pairwise 500kb 5 0.5' have the same effect.) -Note that you need to rerun PLINK using \fB\-\-extract\fR or \fB\-\-exclude\fR on the -\&.prune.in/.prune.out file to apply the list to another computation. -.HP -\fB\-\-r\fR <square | square0 | triangle | inter\-chr> <gz | bin | bin4> <spaces> -.IP -<in\-phase> <dprime> <with\-freqs> <yes\-really> -.HP -\fB\-\-r2\fR <square | square0 | triangle | inter\-chr> <gz | bin | bin4> <spaces> -.IP -<in\-phase> <dprime> <with\-freqs> <yes\-really> -.TP -LD statistic reports. -\fB\-\-r\fR yields raw inter\-variant correlations, while -.TP -\fB\-\-r2\fR reports their squares. -You can request results for all pairs in -.IP -matrix format (if you specify 'bin' or one of the shape modifiers), all -pairs in table format ('inter\-chr'), or a limited window in table format -(default). -* The 'gz' modifier causes the output text file to be gzipped. -* 'bin' causes the output matrix to be written in double\-precision binary -.TP -format, while 'bin4' specifics single\-precision binary. -The matrix is -.IP -square if no shape is explicitly specified. -.IP -* By default, text matrices are tab\-delimited; 'spaces' switches this. -* 'in\-phase' adds a column with in\-phase allele pairs to table\-formatted -.TP -reports. -(This cannot be used with very long allele codes.) -.IP -* 'dprime' adds Lewontin's D\-prime statistic to table\-formatted reports, -.IP -and forces both r/r^2 and D\-prime to be based on the maximum likelihood -solution to the cubic equation discussed in Gaunt T, Rodriguez S, Day I -(2007) Cubic exact solutions for the estimation of pairwise haplotype -frequencies. -.IP -* 'with\-freqs' adds MAF columns to table\-formatted reports. -* Since the resulting file can easily be huge, you're required to add the -.IP -\&'yes\-really' modifier when requesting an unfiltered, non\-distributed all -pairs computation on more than 400k variants. -.IP -* These computations can be subdivided with \fB\-\-parallel\fR (even when the -.IP -\&'square' modifier is active). -.HP -\fB\-\-ld\fR [variant ID] [variant ID] <hwe\-midp> -.IP -This displays haplotype frequencies, r^2, and D' for a single pair of -variants. When there are multiple biologically possible solutions to the -haplotype frequency cubic equation, all are displayed (instead of just the -maximum likelihood solution identified by \fB\-\-r\fR/\-\-r2), along with HWE exact -test statistics. -.HP -\fB\-\-blocks\fR <no\-pheno\-req> <no\-small\-max\-span> -.IP -Estimate haplotype blocks, via Haploview's interpretation of the block -definition suggested by Gabriel S et al. (2002) The Structure of Haplotype -Blocks in the Human Genome. -* Normally, samples with missing phenotypes are not considered by this -.IP -computation; the 'no\-pheno\-req' modifier lifts this restriction. -.IP -* Normally, size\-2 blocks may not span more than 20kb, and size\-3 blocks -.TP -are limited to 30kb. -The 'no\-small\-max\-span' modifier removes these -.IP -limits. -.TP -The .blocks file is valid input for PLINK 1.07's \fB\-\-hap\fR command. -However, -.IP -the \fB\-\-hap\fR... family of flags has not been reimplemented in PLINK 1.9 due to -poor phasing accuracy relative to other software; for now, we recommend -using BEAGLE instead of PLINK for case/control haplotype association -analysis. (You can use '\-\-recode beagle' to export data to BEAGLE 3.3.) -We apologize for the inconvenience, and plan to develop variants of the -\fB\-\-hap\fR... flags which handle pre\-phased data effectively. -.HP -\fB\-\-distance\fR <square | square0 | triangle> <gz | bin | bin4> <ibs> <1\-ibs> -.IP -<allele\-ct> <flat\-missing> -.IP -Write a lower\-triangular tab\-delimited table of (weighted) genomic -distances in allele count units to {output prefix}.dist, and a list of the -corresponding sample IDs to {output prefix}.dist.id. The first row of the -\&.dist file contains a single {genome 1\-genome 2} distance, the second row -has the {genome 1\-genome 3} and {genome 2\-genome 3} distances in that -order, etc. -* It is usually best to perform this calculation on a marker set in -.IP -approximate linkage equilibrium. -.IP -* If the 'square' or 'square0' modifier is present, a square matrix is -.IP -written instead; 'square0' fills the upper right triangle with zeroes. -.IP -* If the 'gz' modifier is present, a compressed .dist.gz file is written -.IP -instead of a plain text file. -.IP -* If the 'bin' modifier is present, a binary (square) matrix of -.IP -double\-precision floating point values, suitable for loading from R, is -instead written to {output prefix}.dist.bin. ('bin4' specifies -single\-precision numbers instead.) This can be combined with 'square0' -if you still want the upper right zeroed out, or 'triangle' if you don't -want to pad the upper right at all. -.IP -* If the 'ibs' modifier is present, an identity\-by\-state matrix is written -.TP -to {output prefix}.mibs. -\&'1\-ibs' causes distances expressed as genomic -.IP -proportions (i.e. 1 \- IBS) to be written to {output prefix}.mdist. -Combine with 'allele\-ct' if you want to generate the usual .dist file as -well. -.IP -* By default, distance rescaling in the presence of missing genotype calls -.IP -is sensitive to allele count distributions: if variant A contributes, on -average, twice as much to other pairwise distances as variant B, a -missing call at variant A will result in twice as large of a missingness -correction. To turn this off (because e.g. your missing calls are highly -nonrandom), use the 'flat\-missing' modifier. -.IP -* The computation can be subdivided with \fB\-\-parallel\fR. -.HP -\fB\-\-distance\-matrix\fR -.HP -\fB\-\-ibs\-matrix\fR -.IP -These deprecated commands are equivalent to '\-\-distance 1\-ibs flat\-missing -square' and '\-\-distance ibs flat\-missing square', respectively, except that -they generate space\- instead of tab\-delimited text matrices. -.HP -\fB\-\-make\-rel\fR <square | square0 | triangle> <gz | bin | bin4> -.IP -<cov | ibc2 | ibc3> -.IP -Write a lower\-triangular variance\-standardized realized relationship matrix -to {output prefix}.rel, and corresponding IDs to {output prefix}.rel.id. -* It is usually best to perform this calculation on a marker set in -.IP -approximate linkage equilibrium. -.IP -* 'square', 'square0', 'triangle', 'gz', 'bin', and 'bin4' act as they do -.IP -on \fB\-\-distance\fR. -.IP -* The 'cov' modifier removes the variance standardization step, causing a -.IP -covariance matrix to be calculated instead. -.IP -* By default, the diagonal elements in the relationship matrix are based on -.HP -\fB\-\-ibc\fR's Fhat1; use the 'ibc2' or 'ibc3' modifiers to base them on Fhat2 -.IP -or Fhat3 instead. -.IP -* The computation can be subdivided with \fB\-\-parallel\fR. -.HP -\fB\-\-make\-grm\-gz\fR <no\-gz> <cov | ibc2 | ibc3> -.HP -\fB\-\-make\-grm\-bin\fR <cov | ibc2 | ibc3> -.HP -\fB\-\-make\-grm\-gz\fR writes the relationships in GCTA's original gzipped list -.IP -format, which describes one pair per line, while \fB\-\-make\-grm\-bin\fR writes them -in GCTA 1.1+'s single\-precision triangular binary format. Note that these -formats explicitly report the number of valid observations (where neither -sample has a missing call) for each pair, which is useful input for some -scripts. -These computations can be subdivided with \fB\-\-parallel\fR. -.HP -\fB\-\-rel\-cutoff\fR {val} -.IP -(alias: \fB\-\-grm\-cutoff\fR) -Exclude one member of each pair of samples with relatedness greater than -the given cutoff value (default 0.025). If no later operation will cause -the list of remaining samples to be written to disk, this will save it to -{output prefix}.rel.id. -Note that maximizing the remaining sample size is equivalent to the NP\-hard -maximum independent set problem, so we use a greedy algorithm instead of -guaranteeing optimality. (Use the \fB\-\-make\-rel\fR and \fB\-\-keep\fR/\-\-remove flags if -you want to try to do better.) -.HP -\fB\-\-ibs\-test\fR {permutation count} -.HP -\fB\-\-groupdist\fR {iters} {d} -.IP -Given case/control phenotype data, these commands consider three subsets of -the distance matrix: pairs of affected samples, affected\-unaffected pairs, -and pairs of unaffected samples. Each of these subsets has a distribution -of pairwise genomic distances; \fB\-\-ibs\-test\fR uses permutation to estimate -p\-values re: which types of pairs are most similar, while \fB\-\-groupdist\fR -focuses on the differences between the centers of these distributions and -estimates standard errors via delete\-d jackknife. -.HP -\fB\-\-regress\-distance\fR {iters} {d} -.IP -Linear regression of pairwise genomic distances on pairwise average -phenotypes and vice versa, using delete\-d jackknife for standard errors. A -scalar phenotype is required. -* With less than two parameters, d is set to {number of people}^0.6 rounded -.TP -down. -With no parameters, 100k iterations are run. -.HP -\fB\-\-regress\-rel\fR {iters} {d} -.IP -Linear regression of pairwise genomic relationships on pairwise average -phenotypes, and vice versa. Defaults for iters and d are the same as for -\fB\-\-regress\-distance\fR. -.HP -\fB\-\-genome\fR <gz> <rel\-check> <full> <unbounded> <nudge> -.IP -Generate an identity\-by\-descent report. -* It is usually best to perform this calculation on a marker set in -.IP -approximate linkage equilibrium. -.IP -* The 'rel\-check' modifier excludes pairs of samples with different FIDs -.IP -from the final report. -.IP -* 'full' adds raw pairwise comparison data to the report. -* The P(IBD=0/1/2) estimator employed by this command sometimes yields -.TP -numbers outside the range [0,1]; by default, these are clipped. -The -.IP -\&'unbounded' modifier turns off this clipping. -.IP -* Then, when PI_HAT^2 < P(IBD=2), 'nudge' adjusts the final P(IBD=0/1/2) -.IP -estimates to a theoretically possible configuration. -.IP -* The computation can be subdivided with \fB\-\-parallel\fR. -.HP -\fB\-\-homozyg\fR <group | group\-verbose> <consensus\-match> <extend> -.IP -<subtract\-1\-from\-lengths> -.HP -\fB\-\-homozyg\-snp\fR [min var count] -.HP -\fB\-\-homozyg\-kb\fR [min length] -.HP -\fB\-\-homozyg\-density\fR [max inverse density (kb/var)] -.HP -\fB\-\-homozyg\-gap\fR [max internal gap kb length] -.HP -\fB\-\-homozyg\-het\fR [max hets] -.HP -\fB\-\-homozyg\-window\-snp\fR [scanning window size] -.HP -\fB\-\-homozyg\-window\-het\fR [max hets in scanning window hit] -.HP -\fB\-\-homozyg\-window\-missing\fR [max missing calls in scanning window hit] -.HP -\fB\-\-homozyg\-window\-threshold\fR [min scanning window hit rate] -.IP -These commands request a set of run\-of\-homozygosity reports, and allow you -to customize how they are generated. -* If you're satisfied with all the default settings described below, just -.TP -use \fB\-\-homozyg\fR with no modifiers. -Otherwise, \fB\-\-homozyg\fR lets you change a -.IP -few binary settings: -* 'group{\-verbose}' adds a report on pools of overlapping runs of -.TP -homozygosity. -(Automatically set when \fB\-\-homozyg\-match\fR is present.) -.IP -* With 'group{\-verbose}', 'consensus\-match' causes pairwise segmental -.IP -matches to be called based on the variants in the pool's consensus -segment, rather than the variants in the pairwise intersection. -.IP -* Due to how the scanning window algorithm works, it is possible for a -.TP -reported ROH to be adjacent to a few homozygous variants. -The 'extend' -.IP -modifier causes them to be included in the reported ROH if that -wouldn't cause a violation of the \fB\-\-homozyg\-density\fR bound. -.IP -* By default, segment bp lengths are calculated as [end bp position] \- -.TP -[start bp position] + 1. -Therefore, reports normally differ slightly -.TP -from PLINK 1.07, which does not add 1 at the end. -For testing -.IP -purposes, you can use the 'subtract\-1\-from\-lengths' modifier to apply -the old formula. -.IP -* By default, only runs of homozygosity containing at least 100 variants, -.TP -and of total length >= 1000 kilobases, are noted. -You can change these -.IP -minimums with \fB\-\-homozyg\-snp\fR and \fB\-\-homozyg\-kb\fR, respectively. -.IP -* By default, a ROH must have at least one variant per 50 kb on average; -.IP -change this bound with \fB\-\-homozyg\-density\fR. -.IP -* By default, if two consecutive variants are more than 1000 kb apart, they -.IP -cannot be in the same ROH; change this bound with \fB\-\-homozyg\-gap\fR. -.IP -* By default, a ROH can contain an unlimited number of heterozygous calls; -.IP -you can impose a limit with \fB\-\-homozyg\-het\fR. -.IP -* By default, the scanning window contains 50 variants; change this with -.HP -\fB\-\-homozyg\-window\-snp\fR. -.IP -* By default, a scanning window hit can contain at most 1 heterozygous -.IP -call and 5 missing calls; change these limits with \fB\-\-homozyg\-window\-het\fR -and \fB\-\-homozyg\-window\-missing\fR, respectively. -.IP -* By default, for a variant to be eligible for inclusion in a ROH, the hit -.IP -rate of all scanning windows containing the variant must be at least -0.05; change this threshold with \fB\-\-homozyg\-window\-threshold\fR. -.HP -\fB\-\-cluster\fR <cc> <group\-avg | old\-tiebreaks> <missing> <only2> -.IP -Cluster samples using a pairwise similarity statistic (normally IBS). -* The 'cc' modifier forces every cluster to have at least one case and one -.IP -control. -.IP -* The 'group\-avg' modifier causes clusters to be joined based on average -.IP -instead of minimum pairwise similarity. -.IP -* The 'missing' modifier causes clustering to be based on -.IP -identity\-by\-missingness instead of identity\-by\-state, and writes a -space\-delimited identity\-by\-missingness matrix to disk. -.IP -* The 'only2' modifier causes only a .cluster2 file (which is valid input -.IP -for \fB\-\-within\fR) to be written; otherwise 2 other files will be produced. -.IP -* By default, IBS ties are not broken in the same manner as PLINK 1.07, so -.TP -final cluster solutions tend to differ. -This is generally harmless. -.IP -However, to simplify testing, you can use the 'old\-tiebreaks' modifier to -force emulation of the old algorithm. -.HP -\fB\-\-pca\fR {count} <header> <tabs> <var\-wts> -.IP -Calculates a variance\-standardized relationship matrix (use \fB\-\-make\-rel\fR or -\fB\-\-make\-grm\-gz\fR to dump it), and extracts the top 20 principal components. -* It is usually best to perform this calculation on a marker set in -.IP -approximate linkage equilibrium. -.IP -* You can change the number of PCs by passing a numeric parameter. -* The 'header' modifier adds a header line to the .eigenvec output file. -.IP -(For compatibility with the GCTA flag of the same name, the default is no -header line.) -.IP -* The 'tabs' modifier causes the .eigenvec file(s) to be tab\-delimited. -* The 'var\-wts' modifier requests an additional .eigenvec.var file with PCs -.IP -expressed as variant weights instead of sample weights. -.HP -\fB\-\-neighbour\fR [n1] [n2] -.IP -(alias: \fB\-\-neighbor\fR) -Report IBS distances from each sample to their n1th\- to n2th\-nearest -neighbors, associated Z\-scores, and the identities of those neighbors. -Useful for outlier detection. -.HP -\fB\-\-assoc\fR <perm | mperm=[value]> <perm\-count> <fisher | fisher\-midp> <counts> -.IP -<set\-test> -.HP -\fB\-\-assoc\fR <perm | mperm=[value]> <perm\-count> <qt\-means> <lin> <set\-test> -.HP -\fB\-\-model\fR <perm | mperm=[value]> <perm\-count> -.IP -<fisher | fisher\-midp | trend\-only> <set\-test> -<dom | rec | gen | trend> -.IP -Basic association analysis report. -Given a case/control phenotype, \fB\-\-assoc\fR performs a 1df chi\-square allelic -test, while \fB\-\-model\fR performs 4 other tests as well (1df dominant gene -action, 1df recessive gene action, 2df genotypic, Cochran\-Armitage trend). -* With 'fisher'/'fisher\-midp', Fisher's exact test is used to generate -.TP -p\-values. -\&'fisher\-midp' also applies Lancaster's mid\-p adjustment. -.IP -* 'perm' causes an adaptive permutation test to be performed. -* 'mperm=[value]' causes a max(T) permutation test with the specified -.IP -number of replications to be performed. -.IP -* 'perm\-count' causes the permutation test report to include counts instead -.IP -of frequencies. -.IP -* 'counts' causes \fB\-\-assoc\fR to report allele counts instead of frequencies. -* 'set\-test' tests the significance of variant sets. Requires permutation; -.IP -can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max. -.IP -* 'dom', 'rec', 'gen', and 'trend' force the corresponding test to be used -.TP -as the basis for \fB\-\-model\fR permutation. -(By default, the most significant -.IP -result among the allelic, dominant, and recessive tests is used.) -.IP -* 'trend\-only' causes only the trend test to be performed. -Given a quantitative phenotype, \fB\-\-assoc\fR normally performs a Wald test. -* In this case, the 'qt\-means' modifier causes trait means and standard -.IP -deviations stratified by genotype to be reported as well. -.IP -* 'lin' causes the Lin statistic to be computed, and makes it the basis for -.IP -multiple\-testing corrections and permutation tests. -.IP -Several other flags (most notably, \fB\-\-aperm\fR) can be used to customize the -permutation test. -.HP -\fB\-\-mh\fR <perm | mperm=[value]> <perm\-count> <set\-test> -.IP -(alias: \fB\-\-cmh\fR) -.HP -\fB\-\-bd\fR <perm | perm\-bd | mperm=[value]> <perm\-count> <set\-test> -.HP -\fB\-\-mh2\fR -.HP -\fB\-\-homog\fR -.IP -Given a case/control phenotype and a set of clusters, \fB\-\-mh\fR computes 2x2xK -Cochran\-Mantel\-Haenszel statistics for each variant, while \fB\-\-bd\fR also -performs the Breslow\-Day test for odds ratio homogeneity. Permutation and -variant set testing based on the CMH (default) or Breslow\-Day (when -\&'perm\-bd' is present) statistic are supported. -The following similar analyses are also available: -* \fB\-\-mh2\fR swaps the roles of case/control status and cluster membership, -.IP -performing a phenotype\-stratified IxJxK Cochran\-Mantel\-Haenszel test on -association between cluster assignments and genotypes. -.IP -* \fB\-\-homog\fR executes an alternative to the Breslow\-Day test, based on -.IP -partitioning of the chi\-square statistic. -.HP -\fB\-\-gxe\fR {covariate index} -.IP -Given both a quantitative phenotype and a case/control covariate loaded -with \fB\-\-covar\fR defining two groups, \fB\-\-gxe\fR compares the regression coefficient -derived from considering only members of one group to the regression -coefficient derived from considering only members of the other. By -default, the first covariate in the \fB\-\-covar\fR file defines the groups; use -e.g. '\-\-gxe 3' to base them on the third covariate instead. -.HP -\fB\-\-linear\fR <perm | mperm=[value]> <perm\-count> <set\-test> -.IP -<genotypic | hethom | dominant | recessive | no\-snp> <hide\-covar> -<sex | no\-x\-sex> <interaction> <beta> <standard\-beta> <intercept> -.HP -\fB\-\-logistic\fR <perm | mperm=[value]> <perm\-count> <set\-test> -.IP -<genotypic | hethom | dominant | recessive | no\-snp> <hide\-covar> -<sex | no\-x\-sex> <interaction> <beta> -.IP -Multi\-covariate association analysis on a quantitative (\fB\-\-linear\fR) or -case/control (\fB\-\-logistic\fR) phenotype. Normally used with \fB\-\-covar\fR. -* 'perm' normally causes an adaptive permutation test to be performed on -.IP -the main effect, while 'mperm=[value]' starts a max(T) permutation test. -.IP -* 'perm\-count' causes the permutation test report to include counts instead -.IP -of frequencies. -.TP -* 'set\-test' tests the significance of variant sets. -Requires permutation; -.IP -can be customized with \fB\-\-set\-p\fR/\-\-set\-r2/\-\-set\-max. -.IP -* The 'genotypic' modifier adds an additive effect/dominance deviation 2df -.IP -joint test (0/1/2 and 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0 -coding instead. If permutation is also requested, these modifiers cause -permutation to be based on the joint test. -.IP -* 'dominant' and 'recessive' specify a model assuming full dominance or -.IP -recessiveness, respectively, for the A1 allele. -.IP -* 'no\-snp' causes regression to be performed only on the phenotype and the -.TP -covariates, without reference to genomic data. -If permutation is also -.IP -requested, results are reported for all covariates. -.IP -* 'hide\-covar' removes covariate\-specific lines from the report. -* By default, sex (male = 1, female = 0) is automatically added as a -.TP -covariate on X chromosome variants, and nowhere else. -The 'sex' modifier -.IP -causes it to be added everywhere, while 'no\-x\-sex' excludes it. -.TP -* 'interaction' adds genotype x covariate interactions to the model. -This -.IP -cannot be used with the usual permutation tests; use \fB\-\-tests\fR to define -the permutation test statistic instead. -.IP -* For logistic regressions, the 'beta' modifier causes regression -.IP -coefficients instead of odds ratios to be reported. -.IP -* With \fB\-\-linear\fR, the 'standard\-beta' modifier standardizes the phenotype -.IP -and all predictors to zero mean and unit variance before regression, and -the 'intercept' modifier adds intercepts to the main report. -.HP -\fB\-\-dosage\fR [allele dosage file] <noheader> <skip0=[i]> <skip1=[j]> <skip2=[k]> -.IP -<dose1> <format=[m]> <Zout> <occur | standard\-beta> <sex> -.HP -\fB\-\-dosage\fR [list file] list <sepheader | noheader> <skip0=[i]> <skip1=[j]> -.IP -<skip2=[k]> <dose1> <format=[m]> <Zout> <occur | standard\-beta> -<sex> -.HP -\fB\-\-write\-dosage\fR -.IP -Process (possibly gzipped) text files with variant\-major allelic dosage -data. This cannot be used with a regular input fileset; instead, you must -*only* specify a .fam and possibly a .map file, and you can't specify any -other commands. -* PLINK 2.0 will have first\-class support for genotype probabilities. An -.IP -equivalent data import flag will be provided then, and \fB\-\-dosage\fR will be -retired. -.IP -* By default, \fB\-\-dosage\fR assumes that only one allelic dosage file should be -.TP -loaded. -To specify multiple files, -.TP -1. create a master list with one entry per line. -There are normally two -.IP -supported formats for this list: just a filename per line, or variant -batch numbers in the first column and filenames in the second. -.IP -2. Provide the name of that list as the first \fB\-\-dosage\fR parameter. -3. Add the 'list' modifier. -.IP -* By default, \fB\-\-dosage\fR assumes the allelic dosage file(s) contain a header -.IP -line, which has 'SNP' in column i+1, 'A1' in column i+j+2, 'A2' in column -i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are -normally zero, but can be changed with 'skip0', 'skip1', and 'skip2' -respectively.) If such a header line is not present, -* when all samples appear in the same order as they do in the .fam file, -.IP -you can use the 'noheader' modiifer. -.IP -* Otherwise, use the 'sepheader' modifier, and append sample ID filenames -.IP -to your 'list' file entries. -.IP -* The 'format' modifier lets you specify the number of values used to -.TP -represent each dosage. -\&'format=1' normally indicates a single 0..2 A1 -.TP -expected count; 'dose1' modifies this to a 0..1 frequency. -\&'format=2' -.IP -(the default) indicates a 0..1 homozygous A1 likelihood followed by a -0..1 het likelihood, while 'format=3' indicates 0..1 hom A1, 0..1 het, -0..1 hom A2. -.IP -* 'Zout' causes the output file to be gzipped. -* Normally, an association analysis is performed. 'standard\-beta' and -.TP -\&'sex' behave as they are supposed to with \fB\-\-linear\fR/\-\-logistic. -(Note -.IP -that \fB\-\-dosage\fR + \fB\-\-sex\fR did NOT work properly in PLINK 1.07.) -.IP -* There are three alternate modes which cause the association analysis to -.IP -be skipped. -* 'occur' requests a simple variant occurrence report. -* \fB\-\-write\-dosage\fR causes a simple merged file matching the 'format' -.IP -specification (not including 'dose1') to be generated. -.IP -* \fB\-\-score\fR applies a linear scoring system to the dosages. -.HP -\fB\-\-lasso\fR [h2 estimate] {min lambda} <report\-zeroes> -.TP -Estimate variant effect sizes via LASSO regression. -You must provide an -.IP -additive heritability estimate to calibrate the regression. -Note that this method may require a very large sample size (e.g. hundreds -of thousands) to be effective on complex polygenic traits. -.HP -\fB\-\-test\-missing\fR <perm | mperm=[value]> <perm\-count> <midp> -.IP -Check for association between missingness and case/control status, using -Fisher's exact test. The 'midp' modifier causes Lancaster's mid\-p -adjustment to be applied. -.HP -\fB\-\-make\-perm\-pheno\fR [ct] -.IP -Generate phenotype permutations and write them to disk, without invoking an -association test. -.HP -\fB\-\-tdt\fR <exact | exact\-midp | poo> <perm | mperm=[value]> -.IP -<parentdt1 | parentdt2 | pat | mat> <set\-test> -.IP -Report transmission disequilibrium test statistics, given case/control -phenotypes and pedigree information. -* A Mendel error check is performed before the main tests; offending -.IP -genotypes are treated as missing by this analysis. -.IP -* By default, the basic TDT p\-value is based on a chi\-square test unless -.IP -you request the exact binomial test with 'exact' or 'exact\-midp'. -.IP -* 'perm'/'mperm=[value]' requests a family\-based adaptive or max(T) -.TP -permutation test. -By default, the permutation test statistic is the -.IP -basic TDT p\-value; 'parentdt1'/'parentdt2' cause parenTDT or combined -test p\-values, respectively, to be considered instead. -.TP -* 'set\-test' tests the significance of variant sets. -This cannot be used -.IP -with exact tests for now. -.IP -The 'poo' modifier causes a parent\-of\-origin analysis to be performed -instead, with transmissions from heterozygous fathers and heterozygous -mothers considered separately. -* The parent\-of\-origin analysis does not currently support exact tests. -* By default, the permutation test statistic is the absolute -.IP -parent\-of\-origin test Z score; 'pat'/'mat' cause paternal or maternal TDT -chi\-square statistics, respectively, to be considered instead. -.HP -\fB\-\-qfam\fR <perm | mperm=[value]> <perm\-count> -.HP -\fB\-\-qfam\-parents\fR <perm | mperm=[value]> <perm\-count> -.HP -\fB\-\-qfam\-between\fR <perm | mperm=[value]> <perm\-count> -.HP -\fB\-\-qfam\-total\fR <perm | mperm=[value]> <perm\-count> -.IP -QFAM family\-based association test for quantitative traits. -* A Mendel error check is performed before the main tests; offending -.IP -genotypes are treated as missing by this analysis. -.TP -* This procedure requires permutation. -\&'perm' and 'perm\-count' have the -.TP -usual meanings. -However, 'mperm=[value]' just specifies a fixed number -.IP -of permutations; the method does not support a proper max(T) test. -.HP -\fB\-\-annotate\fR [PLINK report] <attrib=[file]> <ranges=[file]> <filter=[file]> -.IP -<snps=[file]> <NA | prune> <block> <subset=[file]> <minimal> -<distance> -.TP -Add annotations to a variant\-based PLINK report. -This requires an -.IP -annotation source: -* 'attrib=[file]' specifies a (possibly gzipped) attribute file. -* 'ranges=[file]' specifies a gene/range list file. -(Both source types can be specified simultaneously.) The following options -are also supported: -* 'filter=[file]' causes only variants within one of the ranges in the file -.IP -to be included in the new report. -.IP -* 'snps=[file]' causes only variants named in the file to be included in -.IP -the new report. -.IP -* The 'NA' modifier causes unannotated variants to have 'NA' instead of '.' -.IP -in the new report's ANNOT column, while the 'prune' modifier excludes -them entirely. -.IP -* The 'block' modifier replaces the single ANNOT column with a 0/1\-coded -.IP -column for each possible annotation. -.IP -* With 'ranges', -.IP -* 'subset=[file]' causes only intervals named in the subset file to be -.IP -loaded from the ranges file. -.IP -* interval annotations normally come with a parenthesized signed distance -.IP -to the interval boundary (0 if the variant is located inside the -interval; this is always true without \fB\-\-border\fR). They can be excluded -with the 'minimal' modifier. -.IP -* the 'distance' modifier adds 'DIST' and 'SGN' columns describing signed -.IP -distance to the nearest interval. -.IP -* When \fB\-\-pfilter\fR is present, high p\-values are filtered out. -.HP -\fB\-\-clump\fR [PLINK report filename(s)...] -.IP -Process association analysis report(s) with 'SNP' and p\-value columns, -organizing results by LD\-based clumps. Multiple filenames can be separated -by spaces or commas. -.HP -\fB\-\-gene\-report\fR [PLINK report] [gene range file] -.IP -Generate a gene\-based report from a variant\-based report. -* When \fB\-\-pfilter\fR is present, high p\-values are filtered out. -* When \fB\-\-extract\fR (without 'range') is present, only variants named in the -.HP -\fB\-\-extract\fR file are considered. -.HP -\fB\-\-fast\-epistasis\fR <boost | joint\-effects | no\-ueki> <case\-only> -.IP -<set\-by\-set | set\-by\-all> <nop> -.HP -\fB\-\-epistasis\fR <set\-by\-set | set\-by\-all> -.TP -Scan for epistatic interactions. -\fB\-\-fast\-epistasis\fR inspects 3x3 joint -.IP -genotype count tables and only applies to case/control phenotypes, while -\fB\-\-epistasis\fR performs linear or logistic regression. -* By default, \fB\-\-fast\-epistasis\fR uses the PLINK 1.07 allele\-based test. Two -.IP -newer tests are now supported: 'boost' invokes the likelihood ratio test -introduced by Wan X et al. (2010) BOOST: A Fast Approach to Detecting -Gene\-Gene Interactions in Genome\-wide Case\-Control Studies, while -\&'joint\-effects' applies the joint effects test introduced in Ueki M, -Cordell HJ (2012) Improved statistics for genome\-wide interaction -analysis. -.IP -* The original \fB\-\-fast\-epistasis\fR test normally applies the variance and -.TP -empty cell corrections suggested by Ueki and Cordell's paper. -To disable -.IP -them, use the 'no\-ueki' modifier. -.IP -* 'case\-only' requests a case\-only instead of a case/control test. -* By default, all pairs of variants across the entire genome are tested. -.IP -To just test pairs of variants within a single set, add the 'set\-by\-set' -modifier and load exactly one set with \fB\-\-set\fR/\-\-make\-set; with exactly two -sets loaded, all variants in one set are tested against all variants in -the other. 'set\-by\-all' tests all variants in one set against the entire -genome instead. -.IP -* 'nop' strips p\-values from the main report. -* These computations can be subdivided with \fB\-\-parallel\fR; however... -.HP -\fB\-\-epistasis\-summary\-merge\fR [common file prefix] [ct] -.IP -When a \fB\-\-\fR{fast\-}epistasis job is subdivided with \fB\-\-parallel\fR, the main -report can be assembled at the end by applying Unix 'cat' in the usual -manner, but the .summary.1, .summary.2, ... files may require a specialized -merge. \fB\-\-epistasis\-summary\-merge\fR takes care of the latter. -.HP -\fB\-\-twolocus\fR [variant ID] [variant ID] -.IP -Two\-locus joint genotype count report. -.HP -\fB\-\-score\fR [filename] {i} {j} {k} <header> <sum | no\-sum> -.IP -<no\-mean\-imputation | center> <include\-cnt> -.IP -Apply a linear scoring system to each sample. -The input file should have one line per scored variant. Variant IDs are -read from column #i, allele codes are read from column #j, and scores are -read from column #k, where i defaults to 1, j defaults to i+1, and k -defaults to j+1. -* The 'header' modifier causes the first nonempty line of the input file to -.IP -be ignored; otherwise, \fB\-\-score\fR assumes there is no header line. -.IP -* By default, final scores are averages of the valid per\-variant scores. -.TP -The 'sum' modifier causes sums to be reported instead. -(This cannot be -.TP -used with 'no\-mean\-imputation'. -And for backward compatibility, 'sum' is -.IP -automatically on with dosage data unless 'no\-sum' is specified.) -.IP -* By default, copies of the unnamed allele contribute zero to score, while -.IP -missing genotypes contribute an amount proportional to the loaded (via -\fB\-\-read\-freq\fR) or imputed allele frequency. To throw out missing -observations instead (decreasing the denominator in the final average -when this happens), use the 'no\-mean\-imputation' modifier. -.IP -* Alternatively, you can use the 'center' modifier to shift all scores to -.IP -mean zero. -.TP -* This command can be used with dosage data. -By default, the 'CNT' column -.IP -is omitted from the output file in this case; use 'include\-cnt' to keep -it. -.HP -\fB\-\-write\-var\-ranges\fR [block ct] -.TP -Divide the set of variants into equal\-size blocks. -(Can be used with -.HP -\fB\-\-snps\fR to split a job across multiple machines.) -.PP -The following other flags are supported. (Order of operations is described at -https://www.cog\-genomics.org/plink2/order .) -.HP -\fB\-\-script\fR [fname] : Include command\-line options from file. -.TP -\fB\-\-rerun\fR {log} -: Rerun commands in log (default 'plink.log'). -.TP -\fB\-\-version\fR -: Display only version number before exiting. -.TP -\fB\-\-silent\fR -: Suppress output to console. -.TP -\fB\-\-gplink\fR -: Reserved for interoperation with gPLINK. -.HP -\fB\-\-missing\-genotype\fR [char] : Set missing genotype code (normally '0'). -.TP -\fB\-\-double\-id\fR -: Set both FIDs and IIDs to the VCF/BCF sample ID. -.TP -\fB\-\-const\-fid\fR {ID} -: Set all FIDs to the given constant (default '0'). -.TP -\fB\-\-id\-delim\fR {d} -: Parse sample IDs as [FID][d][IID] (default delim '_'). -.HP -\fB\-\-vcf\-idspace\-to\fR [c] : Convert spaces in sample IDs to the given character. -.HP -\fB\-\-biallelic\-only\fR <strict> <list> : Skip VCF variants with 2+ alt. alleles. -.TP -\fB\-\-vcf\-min\-qual\fR [val] -: Skip VCF variants with low/missing QUAL. -.TP -\fB\-\-vcf\-filter\fR {exception(s)...} -: Skip variants which have FILTER failures. -.TP -\fB\-\-vcf\-half\-call\fR [m] -: Specify how '0/.' and similar VCF GT values should be -handled. The following three modes are supported: -* 'error'/'e' (default) errors out and reports line #. -* 'haploid'/'h' treats them as haploid calls. -* 'missing'/'m' treats them as missing. -.TP -\fB\-\-oxford\-single\-chr\fR [chr nm] : Specify single\-chromosome .gen file with -ignorable first column. -.HP -\fB\-\-oxford\-pheno\-name\fR [col nm] : Import named phenotype from the .sample file. -.TP -\fB\-\-hard\-call\-threshold\fR [val] -: When an Oxford\-format fileset is loaded, calls -.TP -\fB\-\-hard\-call\-threshold\fR random -with uncertainty level greater than 0.1 are -normally treated as missing. You can adjust -this threshold by providing a numeric -parameter, or randomize all calls with -\&'random'. -.HP -\fB\-\-missing\-code\fR {string list} : Comma\-delimited list of missing phenotype -.TP -(alias: \fB\-\-missing_code\fR) -values for Oxford\-format filesets (def. 'NA'). -.TP -\fB\-\-simulate\-ncases\fR [num] -: Set \fB\-\-simulate\fR case count (default 1000). -.TP -\fB\-\-simulate\-ncontrols\fR [n] -: Set \fB\-\-simulate\fR control count (default 1000). -.HP -\fB\-\-simulate\-prevalence\fR [p] : Set \fB\-\-simulate\fR disease prevalence (default 0.01). -.TP -\fB\-\-simulate\-n\fR [num] -: Set \fB\-\-simulate\-qt\fR sample count (default 1000). -.HP -\fB\-\-simulate\-label\fR [prefix] : Set \fB\-\-simulate\fR{\-qt} FID/IID name prefix. -.HP -\fB\-\-simulate\-missing\fR [freq] : Set \fB\-\-simulate\fR{\-qt} missing genotype frequency. -.TP -\fB\-\-allow\-extra\-chr\fR <0> -: Permit unrecognized chromosome codes. The '0' -.TP -(alias: \fB\-\-aec\fR) -modifier causes them to be treated as if they had -been set to zero. -.HP -\fB\-\-chr\-set\fR [autosome ct] <no\-x> <no\-y> <no\-xy> <no\-mt> : -.TP -Specify a nonhuman chromosome set. -The first parameter sets the number of -.IP -diploid autosome pairs if positive, or haploid chromosomes if negative. -Given diploid autosomes, the remaining modifiers indicate the absence of -the named non\-autosomal chromosomes. -.HP -\fB\-\-cow\fR/\-\-dog/\-\-horse/\-\-mouse/\-\-rice/\-\-sheep : Shortcuts for those species. -.TP -\fB\-\-autosome\-num\fR [value] -: Alias for '\-\-chr\-set [value] no\-y no\-xy no\-mt'. -.TP -\fB\-\-cm\-map\fR [fname pattern] {chr} : Use SHAPEIT\-format recombination maps to set -centimorgan positions. To process more than -one chromosome, include a '@' in the first -parameter where the chrom. number belongs, -e.g. 'genetic_map_chr@_combined_b37.txt'. -.TP -\fB\-\-zero\-cms\fR -: Zero out centimorgan positions. -.TP -\fB\-\-pheno\fR [fname] -: Load phenotype data from the specified file, instead of -using the values in the main input fileset. -.TP -\fB\-\-all\-pheno\fR -: For basic association tests, loop through all phenotypes -in \fB\-\-pheno\fR file. -.TP -\fB\-\-mpheno\fR [col] -: Specify phenotype column number in \fB\-\-pheno\fR file. -.TP -\fB\-\-pheno\-name\fR [c] : If \fB\-\-pheno\fR file has a header row, use column with the -given name. -.TP -\fB\-\-pheno\-merge\fR -: When the main input fileset contains an phenotype value -for a sample, but the \fB\-\-pheno\fR file does not, use the -original value instead of treating the phenotype as -missing. -.HP -\fB\-\-missing\-phenotype\fR [v] : Set missing phenotype value (normally \fB\-9\fR). -.TP -\fB\-\-1\fR -: Expect case/control phenotypes to be coded as -0 = control, 1 = case, instead of the usual -0 = missing, 1 = control, 2 = case. -.TP -\fB\-\-make\-pheno\fR [fn] [val] : Define a new case/control phenotype. -If the val -parameter is '*', all samples listed in the given -file are cases, and everyone else is a control. -(Note that, in some shells, it is necessary to -surround the * with quotes.) -Otherwise, all samples with third column entry -equal to the val parameter are cases, and all other -samples mentioned in the file are controls. -.TP -\fB\-\-tail\-pheno\fR [Lt] {Hbt} : Downcode a scalar phenotype to a case/control -phenotype. All samples with phenotype values -greater than Hbt are cases, and all with values -less than or equal to Lt are controls. If Hbt is -unspecified, it is equal to Lt; otherwise, -in\-between phenotype values are set to missing. -.HP -\fB\-\-covar\fR [filename] <keep\-pheno\-on\-missing\-cov> : Specify covariate file. -.TP -\fB\-\-covar\-name\fR [...] -: Specify covariate(s) in \fB\-\-covar\fR file by name. -Separate multiple names with spaces or commas, and -use dashes to designate ranges. -.TP -\fB\-\-covar\-number\fR [...] -: Specify covariate(s) in \fB\-\-covar\fR file by index. -.TP -\fB\-\-within\fR [f] <keep\-NA> -: Specify initial cluster assignments. -.TP -\fB\-\-mwithin\fR [n] -: Load cluster assignments from column n+2. -.TP -\fB\-\-family\fR -: Create a cluster for each family ID. -.TP -\fB\-\-loop\-assoc\fR [f] <keep\-NA> -: Run specified case/control association -commands once for each cluster in the file, -using cluster membership as the phenotype. -.TP -\fB\-\-set\fR [filename] -: Load sets from a .set file. -.TP -\fB\-\-set\-names\fR [name(s)...] -: Load only sets named on the command line. -Use spaces to separate multiple names. -.TP -\fB\-\-subset\fR [filename] -: Load only sets named in the given text file. -.HP -\fB\-\-set\-collapse\-all\fR [set name] : Merge all sets. -.TP -\fB\-\-complement\-sets\fR -: Invert all sets. (Names gain 'C_' prefixes.) -.HP -\fB\-\-make\-set\-complement\-all\fR [s] : \fB\-\-set\-collapse\-all\fR + inversion. -.TP -\fB\-\-make\-set\fR [filename] -: Define sets from a list of named bp ranges. -.TP -\fB\-\-make\-set\-border\fR [kbs] -: Stretch regions in \fB\-\-make\-set\fR file. -.TP -\fB\-\-make\-set\-collapse\-group\fR -: Define sets from groups instead of sets in -\fB\-\-make\-set\fR file. -.TP -\fB\-\-keep\fR [filename] -: Exclude all samples not named in the file. -.TP -\fB\-\-remove\fR [filename] -: Exclude all samples named in the file. -.HP -\fB\-\-keep\-fam\fR [filename] : Exclude all families not named in the file. -.TP -\fB\-\-remove\-fam\fR [fname] -: Exclude all families named in the file. -.HP -\fB\-\-extract\fR <range> [f] : Exclude all variants not named in the file. -.HP -\fB\-\-exclude\fR <range> [f] : Exclude all variants named in the file. -.TP -\fB\-\-keep\-clusters\fR [filename] -: These can be used individually or in -.TP -\fB\-\-keep\-cluster\-names\fR [name(s)...] -combination to define a list of -clusters to keep; all samples not in a -cluster in that list are then excluded. -Use spaces to separate cluster names -for \fB\-\-keep\-cluster\-names\fR. -.TP -\fB\-\-remove\-clusters\fR [filename] -: Exclude all clusters named in the file. -.HP -\fB\-\-remove\-cluster\-names\fR [name(s)...] : Exclude the named clusters. -.TP -\fB\-\-gene\fR [sets...] : Exclude variants not in a set named on the command line. -(Separate multiple set names with spaces.) -.TP -\fB\-\-gene\-all\fR -: Exclude variants which aren't a member of any set. (PLINK -1.07 automatically did this under some circumstances.) -.HP -\fB\-\-attrib\fR [f] {att lst} : Given a file assigning attributes to variants, and a -.TP -\fB\-\-attrib\-indiv\fR [f] {a} -comma\-delimited list (with no whitespace) of -attribute names, remove variants/samples which are -either missing from the file or don't have any of -the listed attributes. If some attribute names in -the list are preceded by '\-', they are treated as -\&'negative match conditions' instead: variants with -all the negative match attributes are removed. -The first character in the list cannot be a '\-', due -to how command\-line parsing works; add a comma in -front to get around this. -.TP -\fB\-\-chr\fR [chrs...] -: Exclude all variants not on the given chromosome(s). -Valid choices for humans are 0 (unplaced), 1\-22, X, Y, XY, -and MT. Separate multiple chromosomes with spaces and/or -commas, and use a dash (no adjacent spaces permitted) to -denote a range, e.g. '\-\-chr 1\-4, 22, xy'. -.TP -\fB\-\-not\-chr\fR [...] -: Reverse of \fB\-\-chr\fR (exclude variants on listed chromosomes). -.TP -\fB\-\-autosome\fR -: Exclude all non\-autosomal variants. -.TP -\fB\-\-autosome\-xy\fR -: Exclude all non\-autosomal variants, except those with -chromosome code XY (pseudo\-autosomal region of X). -.HP -\fB\-\-snps\-only\fR <no\-DI> : Exclude variants with multi\-character allele codes. -.TP -\fB\-\-from\fR [var ID] -: Use ID(s) to specify a variant range to load. When used -.TP -\fB\-\-to\fR -[var ID] together, both variants must be on the same chromosome. -.TP -\fB\-\-snp\fR -[var ID] : Specify a single variant to load. -.HP -\fB\-\-exclude\-snp\fR [] : Specify a single variant to exclude. -.TP -\fB\-\-window\fR -[kbs] : With \fB\-\-snp\fR or \fB\-\-exclude\-snp\fR, loads/excludes all variants -within half the specified kb distance of the named one. -.TP -\fB\-\-from\-bp\fR [pos] -: Use physical position(s) to define a variant range to -.TP -\fB\-\-to\-bp\fR -[pos] load. \fB\-\-from\-kb\fR/\-\-to\-kb/\-\-from\-mb/\-\-to\-mb allow decimal -.TP -\fB\-\-from\-kb\fR [pos] -values. You must also specify a single chromosome (using -.TP -\fB\-\-to\-kb\fR -[pos] e.g. \fB\-\-chr\fR) when using these flags. -.HP -\fB\-\-from\-mb\fR [pos] -.TP -\fB\-\-to\-mb\fR -[pos] -.TP -\fB\-\-snps\fR [var IDs...] -: Use IDs to specify variant range(s) to load or -.TP -\fB\-\-exclude\-snps\fR [...] -exclude. E.g. '\-\-snps rs1111\-rs2222, rs3333, rs4444'. -.TP -\fB\-\-thin\fR [p] -: Randomly remove variants, retaining each with prob. p. -.HP -\fB\-\-thin\-count\fR [n] : Randomly remove variants until n of them remain. -.TP -\fB\-\-bp\-space\fR [bps] : Remove variants so that each pair is no closer than the -given bp distance. (Equivalent to VCFtools \fB\-\-thin\fR.) -.TP -\fB\-\-filter\fR [f] [val(s)...] : Exclude all samples without a 3rd column entry in -the given file matching one of the given -space\-separated value(s). -.TP -\fB\-\-mfilter\fR [n] -: Match against (n+2)th column instead. -.TP -\fB\-\-geno\fR {val} -: Exclude variants with missing call frequencies greater -than a threshold (default 0.1). (Note that the default -threshold is only applied if \fB\-\-geno\fR is invoked without a -parameter; when \fB\-\-geno\fR is not invoked, no per\-variant -missing call frequency ceiling is enforced at all. Other -inclusion/exclusion default thresholds work the same way.) -.TP -\fB\-\-mind\fR {val} -: Exclude samples with missing call frequencies greater than -a threshold (default 0.1). -.TP -\fB\-\-oblig\-missing\fR [f1] [f2] : Specify blocks of missing genotype calls for -\fB\-\-geno\fR/\-\-mind to ignore. The first file should -have variant IDs in the first column and block -IDs in the second, while the second file should -have FIDs in the first column, IIDs in the -second, and block IDs in the third. -.TP -\fB\-\-prune\fR -: Remove samples with missing phenotypes. -.TP -\fB\-\-maf\fR {val} -: Exclude variants with minor allele frequency lower than a -threshold (default 0.01). -.TP -\fB\-\-max\-maf\fR [val] -: Exclude variants with MAF greater than the threshold. -.TP -\fB\-\-maf\-succ\fR -: Rule of succession MAF estimation (used in EIGENSOFT). -Given j observations of one allele and k >= j observations -of the other, infer a MAF of (j+1) / (j+k+2), rather than -the default j / (j+k). -.TP -\fB\-\-read\-freq\fR [fn] : Estimate MAFs and heterozygote frequencies from the given -\fB\-\-freq\fR{x} report, instead of the input fileset. -.TP -\fB\-\-hwe\fR [p] <midp> <include\-nonctrl> : Exclude variants with Hardy\-Weinberg -equilibrium exact test p\-values below a -threshold. -.TP -\fB\-\-me\fR [t] [v] <var\-first> : Filter out trios and variants with Mendel error -rates exceeding the given thresholds. -.HP -\fB\-\-me\-exclude\-one\fR {ratio} : Make \fB\-\-me\fR exclude only one sample per trio. -.TP -\fB\-\-qual\-scores\fR [f] {qcol} {IDcol} {skip} : Filter out variants with -out\-of\-range quality scores. -Default range is now [0, \einfty ). -.TP -\fB\-\-qual\-threshold\fR [min qual score] -: Set \fB\-\-qual\-scores\fR range floor. -.TP -\fB\-\-qual\-max\-threshold\fR [max qual score] -: Set \fB\-\-qual\-scores\fR range ceiling. -.TP -\fB\-\-allow\-no\-sex\fR -: Do not treat ambiguous\-sex samples as having missing -phenotypes in analysis commands. (Automatic /w \fB\-\-no\-sex\fR.) -.TP -\fB\-\-must\-have\-sex\fR -: Force ambiguous\-sex phenotypes to missing on -\fB\-\-make\-bed\fR/\-\-make\-just\-fam/\-\-recode/\-\-write\-covar. -.TP -\fB\-\-filter\-cases\fR -: Include only cases in the current analysis. -.TP -\fB\-\-filter\-controls\fR -: Include only controls. -.TP -\fB\-\-filter\-males\fR -: Include only males. -.TP -\fB\-\-filter\-females\fR -: Include only females. -.TP -\fB\-\-filter\-founders\fR -: Include only founders. -.HP -\fB\-\-filter\-nonfounders\fR : Include only nonfounders. -.TP -\fB\-\-nonfounders\fR -: Include nonfounders in allele freq/HWE calculations. -.TP -\fB\-\-make\-founders\fR <require\-2\-missing> <first> : Clear parental IDs for those -with 1+ missing parent(s). -.TP -\fB\-\-recode\-allele\fR [fn] : With \fB\-\-recode\fR A/A\-transpose/AD, count alleles named in -the file (otherwise A1 alleles are always counted). -.TP -\fB\-\-output\-chr\fR [MT code] : Set chromosome coding scheme in output files by -providing the desired human mitochondrial code. -(Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM', -and 'chrMT'.) -.TP -\fB\-\-output\-missing\-genotype\fR [ch] : Set the code used to represent missing -genotypes in output files (normally the -\fB\-\-missing\-genotype\fR value). -.TP -\fB\-\-output\-missing\-phenotype\fR [s] : Set the string used to represent missing -phenotypes in output files (normally the -\fB\-\-missing\-phenotype\fR value). -.TP -\fB\-\-zero\-cluster\fR [f] : In combination with \fB\-\-within\fR/\-\-family, set blocks of -genotype calls to missing. The input file should have -variant IDs in the first column and cluster IDs in the -second. This must now be used with \fB\-\-make\-bed\fR and no -other output commands. -.TP -\fB\-\-set\-hh\-missing\fR : Cause \fB\-\-make\-bed\fR and \fB\-\-recode\fR to set heterozygous haploid -genotypes to missing. -.HP -\fB\-\-split\-x\fR [bp1] [bp2] <no\-fail> : Changes chromosome code of all X chromosome -.TP -\fB\-\-split\-x\fR [build] <no\-fail> -variants with bp position <= bp1 or >= bp2 -to XY. The following build codes are -supported as shorthand: -* 'b36'/'hg18' = NCBI 36, 2709521/154584237 -* 'b37'/'hg19' = GRCh37, 2699520/154931044 -* 'b38'/'hg38' = GRCh38, 2781479/155701383 -By default, PLINK errors out when no -variants would be affected by \fB\-\-split\-x\fR; -the 'no\-fail' modifier (useful in scripts) -overrides this. -.TP -\fB\-\-merge\-x\fR <no\-fail> -: Merge XY chromosome back with X. -.TP -\fB\-\-set\-me\-missing\fR -: Cause \fB\-\-make\-bed\fR to set Mendel errors to missing. -.TP -\fB\-\-fill\-missing\-a2\fR : Cause \fB\-\-make\-bed\fR to replace all missing calls with -homozygous A2 calls. -.TP -\fB\-\-set\-missing\-var\-ids\fR [t] -: Given a template string with a '@' where the -chromosome code should go and '#' where the bp -coordinate belongs, \fB\-\-set\-missing\-var\-ids\fR -assigns chromosome\-and\-bp\-based IDs to unnamed -variants. -You may also use '$1' and '$2' to refer to -allele names in the template string, and in -fact this becomes essential when multiple -variants share the same coordinate. -.TP -\fB\-\-new\-id\-max\-allele\-len\fR [n] : Specify maximum number of leading characters -from allele names to include in new variant IDs -(default 23). -.HP -\fB\-\-missing\-var\-code\fR [string] : Change unnamed variant code (default '.'). -.TP -\fB\-\-update\-chr\fR -[f] {chrcol} {IDcol} {skip} : Update variant chromosome codes. -.TP -\fB\-\-update\-cm\fR -[f] {cmcol} {IDcol} {skip} : Update centimorgan positions. -.TP -\fB\-\-update\-map\fR -[f] {bpcol} {IDcol} {skip} : Update variant bp positions. -.HP -\fB\-\-update\-name\fR [f] {newcol} {oldcol} {skip} : Update variant IDs. -.HP -\fB\-\-update\-alleles\fR [fname] : Update variant allele codes. -.TP -\fB\-\-allele1234\fR <multichar> : Interpret/recode A/C/G/T alleles as 1/2/3/4. -With 'multichar', converts all A/C/G/Ts in allele -names to 1/2/3/4s. -.HP -\fB\-\-alleleACGT\fR <multichar> : Reverse of \fB\-\-allele1234\fR. -.TP -\fB\-\-update\-ids\fR [f] -: Update sample IDs. -.HP -\fB\-\-update\-parents\fR [f] : Update parental IDs. -.TP -\fB\-\-update\-sex\fR [f] {n} : Update sexes. -Sex (1 or M = male, 2 or F = female, 0 -= missing) is loaded from column n+2 (default n is 1). -.TP -\fB\-\-flip\fR [filename] -: Flip alleles (A<\->T, C<\->G) for SNP IDs in the file. -.TP -\fB\-\-flip\-subset\fR [fn] -: Only apply \fB\-\-flip\fR to samples in \fB\-\-flip\-subset\fR file. -.HP -\fB\-\-flip\-scan\-window\fR [ct+1] : Set \fB\-\-flip\-scan\fR max variant ct dist. (def. 10). -.HP -\fB\-\-flip\-scan\-window\-kb\fR [x] : Set \fB\-\-flip\-scan\fR max kb distance (default 1000). -.HP -\fB\-\-flip\-scan\-threshold\fR [x] : Set \fB\-\-flip\-scan\fR min correlation (default 0.5). -.TP -\fB\-\-keep\-allele\-order\fR -: Keep the allele order defined in the .bim file, -instead of forcing A2 to be the major allele. -.HP -\fB\-\-a1\-allele\fR [f] {a1col} {IDcol} {skip} : Force alleles in the file to A1. -.HP -\fB\-\-a2\-allele\fR [f] {a2col} {IDcol} {skip} : Force alleles in the file to A2. -.TP -\fB\-\-indiv\-sort\fR [m] {f} : Specify FID/IID sort order. -The following four modes -are supported: -* 'none'/'0' keeps samples in the order they were -.TP -loaded. -Default for non\-merge operations. -.IP -* 'natural'/'n' invokes 'natural sort', e.g. -.TP -\&'id2' < 'ID3' < 'id10'. -Default when merging. -.IP -* 'ascii'/'a' sorts in ASCII order, e.g. -.IP -\&'ID3' < 'id10' < 'id2'. -.IP -* 'file'/'f' uses the order in the given file (named -.IP -in the second parameter). -.IP -For now, only \fB\-\-merge\fR/\-\-bmerge/\-\-merge\-list and -\fB\-\-make\-bed\fR/\-\-make\-just\-fam respect this flag. -.TP -\fB\-\-with\-phenotype\fR <no\-parents> <no\-sex | female\-2> : Include more sample info -in new .cov file. -.TP -\fB\-\-dummy\-coding\fR {N} <no\-round> : Split categorical variables (n categories, -2 < n <= N, default N is 49) into n\-1 binary -dummy variables when writing covariate file. -.TP -\fB\-\-merge\-mode\fR [n] -: Adjust \fB\-\-\fR{b}merge/\-\-merge\-list behavior based on a -numeric code. -1 (default) = ignore missing calls, otherwise difference -.IP -\-> missing -.IP -2 = only overwrite originally missing calls -3 = only overwrite when nonmissing in new file -4/5 = never overwrite and always overwrite, respectively -6 = report all mismatching calls without merging -7 = report mismatching nonmissing calls without merging -.TP -\fB\-\-merge\-equal\-pos\fR -: Merge variants with different names but identical -positions. -.TP -\fB\-\-mendel\-duos\fR -: Make Mendel error checks consider samples with only one -parent in the dataset. -.TP -\fB\-\-mendel\-multigen\fR -: Make Mendel error checks consider (great\-)grandparental -genotypes when parental genotype data is missing. -.HP -\fB\-\-ld\-window\fR [ct+1] : Set \fB\-\-r\fR/\-\-r2 max variant ct pairwise distance (usu. 10). -.HP -\fB\-\-ld\-window\-kb\fR [x] : Set \fB\-\-r\fR/\-\-r2 max kb pairwise distance (usually 1000). -.HP -\fB\-\-ld\-window\-r2\fR [x] : Set threshold for \fB\-\-r2\fR report inclusion (usually 0.2). -.TP -\fB\-\-ld\-snp\fR [var ID] -: Set first variant in all \fB\-\-r\fR/\-\-r2 pairs. -.HP -\fB\-\-ld\-snps\fR [vID...] : Restrict first \fB\-\-r\fR/\-\-r2 variant to the given ranges. -.TP -\fB\-\-ld\-snp\-list\fR [f] -: Restrict first \fB\-\-r\fR/\-\-r2 var. to those named in the file. -.TP -\fB\-\-ld\-xchr\fR [code] -: Set Xchr model for \fB\-\-indep\fR{\-pairwise}, \fB\-\-r\fR/\-\-r2, -\fB\-\-flip\-scan\fR, and \fB\-\-show\-tags\fR. -1 (default) = males coded 0/1, females 0/1/2 (A1 dosage) -2 = males coded 0/2 -3 = males coded 0/2, but females given double weighting -.TP -\fB\-\-blocks\-max\-kb\fR [kbs] -: Set \fB\-\-blocks\fR maximum haploblock span (def. 200). -.TP -\fB\-\-blocks\-min\-maf\fR [cutoff] -: Adjust \fB\-\-blocks\fR MAF minimum (default 0.05). -.TP -\fB\-\-blocks\-strong\-lowci\fR [x] -: Set \fB\-\-blocks\fR 'strong LD' CI thresholds (defaults -.TP -\fB\-\-blocks\-strong\-highci\fR [x] -0.70 and 0.98). -.HP -\fB\-\-blocks\-recomb\-highci\fR [x] : Set 'recombination' CI threshold (default 0.90). -.TP -\fB\-\-blocks\-inform\-frac\fR [x] -: Force haploblock [strong LD pairs]:[total -informative pairs] ratios to be larger than this -value (default 0.95). -.TP -\fB\-\-distance\-exp\fR [x] : When computing genomic distances, assign each variant a -weight of (2q(1\-q))^{\-x}, where q is the inferred MAF. -(Use \fB\-\-read\-freq\fR if you want to explicitly specify some -or all of the MAFs.) -.TP -\fB\-\-read\-dists\fR [dist file] {id file} : Load a triangular binary distance matrix -instead of recalculating from scratch. -.TP -\fB\-\-ppc\-gap\fR [val] -: Minimum number of base pairs, in thousands, between -informative pairs of markers used in \fB\-\-genome\fR PPC test. -500 if unspecified. -.TP -\fB\-\-min\fR [cutoff] -: Specify minimum PI_HAT for inclusion in \fB\-\-genome\fR report. -.TP -\fB\-\-max\fR [cutoff] -: Specify maximum PI_HAT for inclusion in \fB\-\-genome\fR report. -.TP -\fB\-\-homozyg\-match\fR [] : Set minimum concordance across jointly homozygous -variants for a pairwise allelic match to be declared. -.TP -\fB\-\-pool\-size\fR [ct] -: Set minimum size of pools in '\-\-homozyg group' report. -.TP -\fB\-\-read\-genome\fR [fn] : Load \fB\-\-genome\fR report for \fB\-\-cluster\fR/\-\-neighbour, instead -of recalculating IBS and PPC test p\-values from scratch. -.TP -\fB\-\-ppc\fR [p\-val] -: Specify minimum PPC test p\-value within a cluster. -.TP -\fB\-\-mc\fR [max size] -: Specify maximum cluster size. -.TP -\fB\-\-mcc\fR [c1] [c2] -: Specify maximum case and control counts per cluster. -.TP -\fB\-\-K\fR [min count] -: Specify minimum cluster count. -.TP -\fB\-\-ibm\fR [val] -: Specify minimum identity\-by\-missingness. -.TP -\fB\-\-match\fR [f] {mv} : Use covariate values to restrict clustering. -Without -\fB\-\-match\-type\fR, two samples can only be in the same cluster -if all covariates match. The optional second parameter -specifies a covariate value to treat as missing. -.TP -\fB\-\-match\-type\fR [f] : Refine interpretation of \fB\-\-match\fR file. -The \fB\-\-match\-type\fR -file is expected to be a single line with as many entries -as the \fB\-\-match\fR file has covariates; '0' entries specify -\&'negative matches' (i.e. samples with equal covariate -values cannot be in the same cluster), '1' entries specify -\&'positive matches' (default), and '\-1' causes the -corresponding covariate to be ignored. -.HP -\fB\-\-qmatch\fR [f] {m} : Force all members of a cluster to have similar -.TP -\fB\-\-qt\fR [fname] -quantitative covariate values. The \fB\-\-qmatch\fR file contains -the covariate values, while the \fB\-\-qt\fR file is a list of -nonnegative tolerances (and '\-1's marking covariates to -skip). -.HP -\fB\-\-pca\-cluster\-names\fR [...] : These can be used individually or in combination -.TP -\fB\-\-pca\-clusters\fR [fname] -to define a list of clusters to use in the basic -\fB\-\-pca\fR computation. (\fB\-\-pca\-cluster\-names\fR expects -a space\-delimited sequence of cluster names, -while \fB\-\-pca\-clusters\fR expects a file with one -cluster name per line.) All samples outside -those clusters will then be projected on to the -calculated PCs. -.TP -\fB\-\-mds\-plot\fR [dims] <by\-cluster> <eigvals> : Multidimensional scaling analysis. -Requires \fB\-\-cluster\fR. -.TP -\fB\-\-cell\fR [thresh] -: Skip some \fB\-\-model\fR tests when a contingency table entry is -smaller than the given threshold. -.TP -\fB\-\-condition\fR [var ID] <dominant | recessive> : Add one variant as a \fB\-\-linear\fR -or \fB\-\-logistic\fR covariate. -.TP -\fB\-\-condition\-list\fR [f] <dominant | recessive> : Add variants named in the file -as \fB\-\-linear\fR/\-\-logistic covs. -.TP -\fB\-\-parameters\fR [...] -: Include only the given covariates/interactions in the -\fB\-\-linear\fR/\-\-logistic models, identified by a list of -1\-based indices and/or ranges of them. -.TP -\fB\-\-tests\fR <all> {...} : Perform a (joint) test on the specified term(s) in the -\fB\-\-linear\fR/\-\-logistic model, identified by 1\-based -indices and/or ranges of them. If permutation was -requested, it is based on this test. -* Note that, when \fB\-\-parameters\fR is also present, the -.IP -indices refer to the terms remaining AFTER pruning by -\fB\-\-parameters\fR. -.IP -* You can use '\-\-tests all' to include all terms. -.TP -\fB\-\-vif\fR [max VIF] -: Set VIF threshold for \fB\-\-linear\fR multicollinearity check -(default 50). -.TP -\fB\-\-xchr\-model\fR [code] : Set the X chromosome \fB\-\-linear\fR/\-\-logistic model. -0 = skip sex and haploid chromosomes -1 (default) = add sex as a covariate on X chromosome -2 = code male genotypes 0/2 instead of 0/1 -3 = test for interaction between genotype and sex -.TP -\fB\-\-lasso\-select\-covars\fR {cov(s)...} : Subject some or all covariates to LASSO -model selection. -.TP -\fB\-\-adjust\fR <gc> <log10> <qq\-plot> -: Report some multiple\-testing corrections. -.TP -\fB\-\-lambda\fR [val] -: Set genomic control lambda for \fB\-\-adjust\fR. -.TP -\fB\-\-ci\fR [size] -: Report confidence intervals for odds ratios. -.TP -\fB\-\-pfilter\fR [val] -: Filter out association test results with higher p\-values. -.HP -\fB\-\-aperm\fR [min perms \- 1] {max perms} {alpha} {beta} {init interval} {slope} : -.IP -Set up to six parameters controlling adaptive permutation tests. -* The first two control the minimum and maximum number of permutations that -.IP -may be run for each variant; default values are 5 and 1000000. -.TP -* The next two control the early termination condition. -A -.IP -100% * (1 \- beta/2T) confidence interval is calculated for each empirical -p\-value, where T is the total number of variants; whenever this -confidence interval doesn't contain alpha, the variant is exempted from -further permutation testing. Default values are 0 and 1e\-4. -.TP -* The last two control when the early termination condition is checked. -If -.IP -a check occurs at permutation #p, the next check occurs after -[slope]p + [init interval] more permutations (rounded down). Default -initial interval is 1, and default slope is 0.001. -.TP -\fB\-\-mperm\-save\fR -: Save best max(T) permutation test statistics. -.HP -\fB\-\-mperm\-save\-all\fR : Save all max(T) permutation test statistics. -.TP -\fB\-\-set\-p\fR [p\-val] -: Adjust set test significant variant p\-value ceiling -(default 0.05). -.TP -\fB\-\-set\-r2\fR {v} <write> -: Adjust set test significant variant pairwise r^2 -ceiling (default 0.5). 'write' causes violating -pairs to be dumped to {output prefix}.ldset. -.TP -\fB\-\-set\-max\fR [ct] -: Adjust set test maximum # of significant variants -considered per set (default 5). -.HP -\fB\-\-set\-test\-lambda\fR [v] : Specify genomic control correction for set test. -.TP -\fB\-\-border\fR [kbs] -: Extend \fB\-\-annotate\fR range intervals by given # kbs. -.HP -\fB\-\-annotate\-snp\-field\fR [nm] : Set \fB\-\-annotate\fR variant ID field name. -.HP -\fB\-\-clump\-p1\fR [pval] : Set \fB\-\-clump\fR index var. p\-value ceiling (default 1e\-4). -.HP -\fB\-\-clump\-p2\fR [pval] : Set \fB\-\-clump\fR secondary p\-value threshold (default 0.01). -.TP -\fB\-\-clump\-r2\fR [r^2] -: Set \fB\-\-clump\fR r^2 threshold (default 0.5). -.TP -\fB\-\-clump\-kb\fR [kbs] -: Set \fB\-\-clump\fR kb radius (default 250). -.TP -\fB\-\-clump\-snp\-field\fR [n...] -: Set \fB\-\-clump\fR variant ID field name (default -\&'SNP'). With multiple field names, earlier names -take precedence over later ones. -.TP -\fB\-\-clump\-field\fR [name...] -: Set \fB\-\-clump\fR p\-value field name (default 'P'). -.TP -\fB\-\-clump\-allow\-overlap\fR -: Let \fB\-\-clump\fR non\-index vars. join multiple clumps. -.TP -\fB\-\-clump\-verbose\fR -: Request extended \fB\-\-clump\fR report. -.TP -\fB\-\-clump\-annotate\fR [hdr...] : Include named extra fields in \fB\-\-clump\-verbose\fR and -\fB\-\-clump\-best\fR reports. (Field names can be -separated with spaces or commas.) -.TP -\fB\-\-clump\-range\fR [filename] -: Report overlaps between clumps and regions. -.HP -\fB\-\-clump\-range\-border\fR [kb] : Stretch regions in \fB\-\-clump\-range\fR file. -.TP -\fB\-\-clump\-index\-first\fR -: Extract \fB\-\-clump\fR index vars. from only first file. -.TP -\fB\-\-clump\-replicate\fR -: Exclude clumps which contain secondary results -from only one file. -.TP -\fB\-\-clump\-best\fR -: Report best proxy for each \fB\-\-clump\fR index var. -.TP -\fB\-\-gene\-list\-border\fR [kbs] -: Extend \fB\-\-gene\-report\fR regions by given # of kbs. -.TP -\fB\-\-gene\-subset\fR [filename] -: Specify gene name subset for \fB\-\-gene\-report\fR. -.TP -\fB\-\-gene\-report\-snp\-field\fR [] : Set \fB\-\-gene\-report\fR variant ID field name (default -\&'SNP'). Only relevant with \fB\-\-extract\fR. -.TP -\fB\-\-gap\fR [kbs] -: Set '\-\-fast\-epistasis case\-only' min. gap (default 1000). -.TP -\fB\-\-epi1\fR [p\-value] : Set \fB\-\-\fR{fast\-}epistasis reporting threshold (default -5e\-6 for 'boost', 1e\-4 otherwise). -.HP -\fB\-\-epi2\fR [p\-value] : Set threshold for contributing to SIG_E count (def. 0.01). -.TP -\fB\-\-je\-cellmin\fR [n] : Set required number of observations per 3x3x2 contingency -table cell for joint\-effects test (default 5). -.HP -\fB\-\-q\-score\-range\fR [range file] [data file] {i} {j} <header> : -.IP -Apply \fB\-\-score\fR to subset(s) of variants in the primary score list based -on e.g. p\-value ranges. -* The first file should have range labels in the first column, p\-value -.IP -lower bounds in the second column, and upper bounds in the third column. -Lines with too few entries, or nonnumeric values in the second or third -column, are ignored. -.IP -* The second file should contain a variant ID and a p\-value on each -.TP -nonempty line (except possibly the first). -Variant IDs are read from -.IP -column #i and p\-values are read from column #j, where i defaults to 1 and -j defaults to i+1. The 'header' modifier causes the first nonempty line -of this file to be skipped. -.TP -\fB\-\-parallel\fR [k] [n] : Divide the output matrix into n pieces, and only compute -the kth piece. The primary output file will have the -piece number included in its name, e.g. plink.rel.13 or -plink.rel.13.gz if k is 13. Concatenating these files -in order will yield the full matrix of interest. (Yes, -this can be done before unzipping.) -N.B. This generally cannot be used to directly write a -symmetric square matrix. Choose square0 or triangle -shape instead, and postprocess as necessary. -.TP -\fB\-\-memory\fR [val] -: Set size, in MB, of initial workspace malloc attempt. -(Practically mandatory when using GNU parallel.) -.TP -\fB\-\-threads\fR [val] -: Set maximum number of concurrent threads. -.TP -\fB\-\-d\fR [char] -: Change variant/covariate range delimiter (normally '\-'). -.TP -\fB\-\-seed\fR [val...] -: Set random number seed(s). Each value must be an -integer between 0 and 4294967295 inclusive. -.TP -\fB\-\-perm\-batch\-size\fR [val] : Set number of permutations per batch for some -permutation tests. -.TP -\fB\-\-debug\fR -: Use slower, more crash\-resistant logging method. -.PP -For further documentation and support, consult the main webpage -(https://www.cog\-genomics.org/plink2 ) and/or the mailing list -(https://groups.google.com/d/forum/plink2\-users ). -.SH "SEE ALSO" -The full documentation for -.B PLINK -is maintained as a Texinfo manual. If the -.B info -and -.B PLINK -programs are properly installed at your site, the command -.IP -.B info PLINK -.PP -should give you access to the complete manual. diff --git a/debian/rules b/debian/rules index d029f26..b05d628 100755 --- a/debian/rules +++ b/debian/rules @@ -13,5 +13,9 @@ override_dh_auto_clean: dh_auto_clean rm -f plink1.9 +override_dh_install: + help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1 + dh_install + get-orig-source: uscan --verbose --force-download --repack --compress xz diff --git a/debian/tests/output_tests/README.out b/debian/tests/output_tests/README similarity index 61% rename from debian/tests/output_tests/README.out rename to debian/tests/output_tests/README index 657830b..beed38c 100644 --- a/debian/tests/output_tests/README.out +++ b/debian/tests/output_tests/README @@ -1,10 +1,10 @@ -# Output files (i.e. plink.assoc and plink.frq) were generated following: +# Output files (i.e. expected.plink.assoc and expected.plink.frq) were generated following: wget https://www.cog-genomics.org/static/bin/plink141220/plink_linux_x86_64.zip unzip plink_linux_x86_64.zip ./plink --file toy --freq -mv plink.freq expected.plink.freq +mv plink.frq expected.plink.frq ./plink --file toy --assoc mv plink.assoc expected.plink.assoc diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis index 51435ea..71ba2d1 100644 --- a/debian/tests/run-sample-analysis +++ b/debian/tests/run-sample-analysis @@ -11,14 +11,14 @@ fi cd $ADTTMP cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP -PLINK2_TEST='plink1.9 --file toy' +PLINK19_TEST='plink1.9 --file toy' # Allele frequencies -$PLINK2_TEST --freq +$PLINK19_TEST --freq diff plink.frq expected.plink.frq # Case/control or QTL association -$PLINK2_TEST --assoc +$PLINK19_TEST --assoc diff plink.assoc expected.plink.assoc rm -f $ADTTMP/* -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/plink1.9.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
