V1.07 (10-Oct-2009) Added --meta-analysis function Added --annotate function Added --dosage, --write-dosage, etc Added --Z-genome and ability to read compressed .genome.gz Added --simulate-qt to simulate quantitative trait data Added --recode-rlist and --recode-lgen/--with-reference Added preliminary ZLIB support for reading and writing compressed files directly Added --standard-beta for --linear Added --counts to modify --assoc output Added dosage-based score analysis Changed how options are passed to commands Changed order of --reference-allele and --freq, so that the reference is now fixed prior to calculating and reporting allele frequencies Improved speed of binary file merging MAF-based SNP removal for --indep-pairwise option Fixed bug in --blocks routine Fixed bug in --adjust with quantitative trait --assoc Fixed bug in --fisher and --adjust Fixed bug in --set-test with selection of SNPs in LE V1.06 (24-Apr-2009) Added --show-tags and modifiers, including --list-all Added --blocks command Added --hap-logistic and --hap-linear (with support for covariates and permutation) Added --hap-omnibus that modifies --hap-linear and --hap-logistic Add multiple sizes for sliding window (--hap-window 1,2,3) Fixed issue with D' calculation in --ld command Added --inter-chr option Now enable --ci to work with --chap Added --id-dict, --id-match, --id-replace, --id-alias, --id-table, --id-lookup, etc Added SVD speedup using LAPACK compile-time option Added --reference {file} to complement --lfile Added --allele-count and --compound-genotype support for LGEN files Added --attrib and --attrib-indiv options Added --thin command to prune SNPs randomly Added --hide-covar option for GLM tests Added --make-perm-pheno {N} to create plink.pphe Added --cnv-check-no-overlap Fixed bug that stopped --cnv-method2 from working Can now make sets on-the-fly; added --write-set option Added --make-set-complement {label} Now added a group field to ranges; added --make-set-collapse-group, --make-set-complement-group Fixed issue when mapping ranges to SNPs, would not properly include all end SNPs Fixed it that --range can take >3 cols (--extract file.txt --range ) Added --update-pheno (i.e. similar to --pheno, but doesn't set to missing all non-included people Fixed bug in --update-sex and --update-parents Fixed problem with --update-chr Changed basic --assoc OR calculation to avoid int size limits in v. large samples Changed --model --perm to only consider ALLELIC, DOM, REC (not GENO) Add chr XY for --dog Added --mouse support Fixed input to now allow comment lines (starting with #) in MAP files Added --R-port command Skip zero-ing MEs when rel-check/genome mode Add --q-score-range and --q-score-file options to modify --score Added --simulate-haps, and format/error checks for --simulate files V1.05 (11-Dec-2008) Added support for multiple return values from R-plugins; changed basic protocol Added --beta modifier to --logistic, to return beta coefficients, not odds ratios Fixed minor inconsistencies in --cnv-freq-include-exact: now --cnv-freq-exclude-above 1 equals --cnv-freq-include-exact 1 when used with default overlap thresholds Fixed problem with HWE output Added --cnv-test-region option for CNV mapping Added the --subset command to work with --set Changed --clump-best to preferentially take the same SNP Added option to downweight set-based tests with --lambda Added option --reference-allele to specify manually which is reference allele A1, i.e. instead of minor allele Added support for --rice chromosomes Added --ld-snp-list option Added --make-set-collapse Added --update-alleles, --update-chr, --update-name, --update-ids, --update-sex and --update-parents The --pfilter command now works for --mh Fixed problem with the --hap-tdt command (wasn't working in 1.04 at all) Added support for SNP-specific and genotype-specific quality score filters (--qual-scores and --qual-geno-scores, with corresponding commands --qual-threshold and --qual-max-threshold and --qual-geno-threshold and --qual-geno-max-threshold Made default --score behavior to impute missing genotype scores based on sample frequency, unless --score-no-mean-imputation specified Fixed minor issue with --simulation routine (now we do not assume HWE holds within cases and controls, but only in the population as a whole). Output format of .genome file is changed Modified --genome to display the type of relationship, and expected IBD sharing level, if pair are in same family; also changed output format Added --rel-check modifier to --genome, so that only pairs within the same FID code are considered Modified --read-genome option to accept different format .genome files, by looking for header rows rather than assuming fixed column number/order Added --set-table command to make a SNP by SET matrix Added --tucc option to make pseudo case/control units from trio data V1.04 (26-Aug-2008) Added -gene-report function (with --gene-list, etc) Added --cnv-subset option Added --cnv-verbose-report-regions option Added --clump-best, --clump-range and --clump-range-border Added new LD-aware set-based test and functions --set-p, --set-r2 Added ability to include --covar with --gvar Added --flip-subset option, to flip strand only for some individuals Added --flip-scan procedure, to identify likely strand-flip errors Added --mperm-save and --mperm-save-all options Now reports sample summary after filtering for QTs, as for case/control data Now --pfilter works on .adjusted output files also Changed default behavior to not set pheotype to missing if sex code is missing Changed --recode, etc, output names to plink.ped, etc, rather than plink.recode.ped Added --must-have-sex option to set phenotype to missing when recoding data Added --make-pheno {file} * feature to set as cases people in {file}, else control N_GENO field is now always reported in the missing data output Added fields PHOM and PHET to .hom output (and modified --read-homozyg also) Added function --compound-genotype to allele AG, 11, 00, etc in PED files only Changed default thresholds (to be similar to --all) Added --output-missing-phenotype and --output-missing-genotype options Added --keep-allele-order to stop flipping of allele codes when minor allele frequency is greater than 0.5 Added --proxy-b-r2 to specify alternate proxy parameters for rarer alleles Added allele codes and frequencies to --homog output files Added allele code fields to --hardy and --model output Fixed female Y chromosome genotype rate counting Fixed a problem with --proxy-glm and missing haplotypic data Fixed --R function to send counts of minor, not major, allele Fixed issue with missing genotypes and --gvar association statistics Fixed minor bug with --hardy2 and --hwe2 Fixed problem when --sex used with --chap test Fixed problem with --qfam routine when there are no valid observations Fixed a bug with the --score function Fixed a bug with --hap-impute when used on the X chromosome Fixed a bug in the CNV frequency filter commands Corrected mislabelling of distances/similarities for IBM clustering Removed Hotelling's T2 test from this version Updated the --lookup routines; changed the backend server considerably Updated Rserve client code for use with Rserve version 0.5.2 Added gene-lists to resources section on web Updated HapMap resource to latest release V1.03 (10-Jun-2008) Added teaching material/tutorial to resources section of web Added --write-cluster, which can handle strings Added --cnv-freq-exclude-exact and --cnv-freq-include-exact Added --cnv-region-overlap Displays type and score display in --segment-group for CNVs Fixed problem with --read-freq Fixed problem with --hethom and X chromosome data Fixed problem when --condition and --genotypic used together Added --genome-minimal and --read-genome-minimal Now possible to --filter on strings and lists of strings Added --make-pheno command to generate a binary phenotype given string filter Allow --keep and --remove files to have additional columns beyond two Additional case/control statistics given in LOG after filtering Fixed a bug in the --hap-tdt and --proxy-tdt analyses Added the --make-set and --make-set-border commands Added --lookup-kb and --lookup-gene-kb Added --lookup-gene-list (to create a SET file) Added additional output information to SNP and gene lookups Added --ld-snp command to modify the behaviour of --r2 LD pruning now considers non-autosomal markers Fixed some issues with non-human data and the IBS/IBD calculation (previously skipped chromosomes over 22) V1.02 (27-Mar-2008) Added beta versions of CNV and generic variant commands, described here Created a PDF version of the web page Added --hethom flag to modify --genotypic Added --seed to specify a fixed random seed Added --recode-allele to modify --recodeA Fixed issue with --clump-index-first option Enabled PED files to be input from standard input (--ped -) Fixed potential error in --chap output when test not defined V1.01 (28-Jan-2008) Added --dummy-coding modifier for --write-covar Added --upate-map Outputs phenotype names for --all-pheno if given Reworked --mds-plot and --mds-cluster option to work with --within and without re-running the clustering Fixed --qfam issues with permutation test Changed defaults for --proxy-assoc and --proxy-impute Changed direction of allele coding for proxy association options Changed --proxy-r2-filter command (3 parameters) and naming Changed syntax for proxy association options, --proxy-r2, etc Added --proxy-glm method Fixed problems with --hap-impute Fixed problem with --hap-window Issue with hyphens in SNP names and use as range delimiter (--d) Fixed issue with numeric chromosome codes greater than 22 and --file Changed output format of TDT and CMH commands Make monomorphic SNPs have missing alleles in output if forced Fixed minor problem with --bmerge when more than 2 alleles seen per SNP Physical position output correctly with --genotypic option Changed threshold to print NA in logistic Changed headers BETA or OR in GLM output for clarity Now --recodeA and --recodeAD count number of minor alleles Added --sheep option Fixed problem with --homozyg V1.00 (4-Dec-2007) Added conditional haplotype-based testing (--chap) Added simple data simulation option (--simulate) Added/extended SNP imputation functions (--proxy-assoc and --proxy-impute) Added LD-based results clumping procedure (--clump) Added option to select specific covariates (--values) Added ability to specify lists and ranges of SNPs (--snps) Added ability to select ranges based on regions (--range) Added proxy selection features based on LD (--proxy-r2-filter) Added simple "risk-profile" tool (--score) Fixed issue with scaling of covariates in GLMs Added --rerun option to repeat analysis given LOG file Added --write-snplist option Fixed dirction-of-effect error in haplotypic QTL test Enabled --fisher to work with --model Made variance inflation factor default value less stringent Fixed some problems with haplotype TDT Fixed problem with slightly different p-values for QTL tests from --adjust Fixed bug in --all-pheno option when used with disease traits Fixed bug in --epistasis routine regarding handling of missing data V0.99s (26-July-2007) Added SNP annotation --lookup set of options Added proxy assocition functions (--proxy-assoc, etc) Added extensible R plugin functionality (--R) Added --lfile option for long-format input Fixed problem with all-male or all-female X chromosome test Added r-squared calculation for two SNPs based on haplotype frequencies Added geno-grouping speedup to E-M algorithm; fixed minor problem with treatment of missing genotype data Added --oblig-missing and --oblig-cluster options, to specify obligatory-missing genotypes Added --impute-sex option Added concordance calculation to --merge-mode 6 and 7 Added haplotype support for X and haploid chromosomes Added haplotype support for quantitative trait analysis Mendel error filter now zero's out the people implicated as per heurtistic described here Fixed output commands to use user-defined missing phenotype and genotype values Added dominant and recessive models for --linear and --logistic Improved convergence of EM haplotyping routine Fixed minor bug in --parameters function Added --lambda option to fix genomic control factor Added --log10 option to change output in *.adjusted Added --horse species option Added --qq-plot function Added --loop-assoc option Added --distance-matrix option Changed implementation and interface of the --homozyg-* methods Enabled permutation and set-tests with --dfam Added ability to constrain --cluster with --within Added --recode-bimbam, --recode-fastphase and --recode-structure options Fixed minor issue with --het command Added --liability option Fixed issue with --genotypic and --covar Fixed issue with --dfam V0.99r (29-April-2007) Added --parameters and --tests options Added --zero-cluster option Added --no-fid, --no-parents, --no-sex and --no-pheno options Added --with-phenotype flag to modify --write-covar Now give a warning if fileroots contain a fullstop/period character Added --fisher for Fisher's exact test; use this in --test-missing Added --set-test option DFAM can include unrelateds (possibly in clusters) as well as families in a combined test Improved multicollinearity check in linear model tests Added --all-pheno option for some tests Enabled permutation for --mh Added XY and MT chromosome support Fixed problem with --hap-window introduced in 0.99q Fixed --homog for X and changed output format Fixed problem with --out and --script introduced in 0.99q V0.99q (3-March-2007) Support for PED files larger than 4GB Added --tfile to load transposed (row=SNP,column=person) files (i.e. as from --recode --transpose) Added --recodeA option (like --recodeAD but only output additive components) Added --write-covar option and also ability to include covariate files when recoding or making binary files Add simple filters: --filter-cases, --filter-controls, --filter-males, --filter-females, --filter-founders and --filter-nonfounders Added weighted multimarker tests with --whap Added X chromosome and haploid models for --linear and --logistic with --xchr-model Add --set-me-missing -- now, by default, remaining (i.e. for SNPs/individuals not removed) Mendel errors are not fixed to zero when recoding (--make-bed, etc) a file and filtering on --me. Fixed bug in loading of covariates which made missing phenotypes Changed implementation of --fast-epistasis Fixed minor --bmerge issue with monomorphic alleles in offspring-only subsamples Added --allele1234 and --alleleACGT options Fixed CMH output to NA rather than -9 Added web-based context-specific warnings V0.99p (16-January-2007) Fixed bug in loading of covariates which made missing phenotypes no longer missing (e.g. -9 phenotype would have been treated literally as -9) Fixed bug in --bmerge function when merged-in SNPs already exist Added --transpose option to modify --recode Fixed bug in --genotypic option that lead to incorrect results Added --test-all option for --linear and --logistic Changed --fast-epistasis to use correlational test Added --ci support for --linear and --logistic Added --mds-plot option Now allow --remove and --keep together (similarly for --extract and --exclude Added --genome-lists option to facilitate parallization of --genome Added lower pool size in pool segment output, with --pool-size option Added odds ratio calculation for --model tests Modified --qfam within test (only model W) Added --check-sex option Cleaned up excessive memory use issue when merging multiple files Added speed-up and bug fixes to QFAM routines Added gPLINK compatibility via --gplink flag Now treats half-missing genotypes, e.g. A 0 as missing rather than giving an error (haploid genotypes should still be coded as homozygous) Recode file options (--make-bed, --recode, etc) now do not automatically set haploid heterozygous genotypes to missing, unless --set-hh-missing specified No longer sets p-values <1e-16 to 0 Now use t-statistic for QTL test Improved verbose segmental output (separate files) Added --filter and --mfilter options V0.99o 27-November-2006 Permutation applicable to --test-missing option Added --twolocus output option Added --overlap option Added --logistic and --linear options Added --genotypic and --interaction options Reframed --homozyg tests Added epistasis using linear (QT) and logistic regression models Fixed bug in haplotype-based TDT test (counted transmissions to unaffecteds) IBD estimation adjusted, and fixed a minor bug V0.99n 11-October-2006 Added option to print warning when duplicate individual or marker IDs are found Added --read-segment option Changed output format of HWE and genotypic/model association tests Implemented new bias-correct IBD estimators Fixed minor bug that could cause problems when merging datasets on some platforms Large restructuring of haplotype inference code Added --test-mishap option Added --indep-pairwise option Added --hap-window option Added --ld-window option Added --plist option Added --read-genome option Added --map3 option V0.99m 23-August-2006 Added --gene extraction option Fixed bug affecting labels after set pruning Added --list output option Added --counts option to modify --freq Fixed bug in the Hotelling's T(2) test handling of missing genotypes Added permutation options for --model Fixed minor bug introduced in v0.99l that caused crash when attempting a set-based TDT analysis Altered some field headers in various output files for greater consistency V0.99l 27-July-2006 Added --bmerge option to merge in a binary file Added framework for QFAM test (option not yet available in release version) Added Wiggington et al (AJHG, 2005) exact Hardy-Weinberg calculation Added --from-kb etc options to select regions V0.99j 14-July-2006 Added --window option to extract a +/- X kb region around a given SNP Fixed bug which made set VIF pruning fail with a set containing a single SNP Redircted ambiguous sex and no-non-missing-founders messages to files (plink.nosex and plink.nof) rather than to plink.log Fixed bug in HWE tests which meant non-founders were included V0.99i 5-July-2006 Improved parsing of PED and haplotype specification files; fixed some minor bugs since 0.99h in this regard, mainly DOS versus UNIX issues Fixed bug in haploTDT routine Implemented gene-based canonical correlation test within PLINK (previously, an R script was generated and this analysis was performed externally) Added feature to scan genome and extract a set of SNPs that are relatively uncorrelated with each other (sliding window based on VIF; implemented in the --indep option) V0.99h 29-June-2006 Added option to prune SNPs based on LD (i.e. select an independent subset of SNPs) using the --indep option Fixed bug that occurred when creating a binary map file if a SNP had no non-missing alleles (i.e. previously one allele field was left blank, meaning that the file would not be properly read in subsequently) Improved Hotelling's T(2) calculation -- now it better handles highly or completely correlated SNPs Added singular value decomposition routines and variance inflation calculation Add --allow-no-sex option to differently handle individuals with ambiguous sex codes Fixed bug in --r and --r2 routines V0.99g 20-June-2006 Implemented web-based version checking Fixed error in which families counted twice when filtering on Mendel errors and performing TDT also Added column count check for PED files Allowed comments in PED files (lines starting #) for basic input and merge commands Fixed specification of --gap for case-only epistasis tests -- using kb now, not bp V0.99f 12-June-2006 Fixed bug that TDT in version 0.99e (but not prior versions), that meant that transmissions to unaffecteds as well as affecteds were counted Improved parsing of --merge-list for end-of-file V0.99e 9-June-2006 Improved efficiency of haplotype phase routine Added nearest neighbour identification in --neighbour routine, and fixed a minor bug Added support for haplotypic TDT test Fixed error in homozygosity-run analysis Fixed error in handling of monomorphic variants when creating a binary map file Added --snp option to select single SNPs Added out-of-memory warning V0.99c 23-May-2006 Fixed error in conversion from SNP-major to individual-major data representations that effected Mendel error check routines V0.99b 16-May-2006 Fixed error in Hardy-Weinberg calculations for quantitative traits Implemented --nudge and --impossible features for IBD calculation V0.99 30-Apr-2006 Major internal restructuring to hold data in either row-major or column-major formats, depending on choice of analysis (i.e. order genotypes either by individual or by SNP in memory). Added ability to stratify summary statistics by a cluster variable Improved parsing of haplotypes ( creates .mishap file for mis-specified haplotypes) Fixed bug in CMH tests (problem with individuals who were not assigned to a cluster) Fixed problem with extracting SNPs and individuals with binary PED files V0.98 19-Apr-2006 Added support for adjusted significance test calculation (Bonferroni, FDR, Sidak, etc) Added --script feature to allow long command lines Added --1 feature to allow for 0/1 coding of affection variables Added --tab feature to control field delimiters in recoded PED files Added proper support for combined label-swapping and gene-dropping permutation (--swap-parents, --swap-sibs and --swap-unrel Corrected bug in filters for binary files that aren't in genomic order (i.e. those that result from merge operations). V0.97 10-Apr-2006 Added Hotelling's T2 test for multilocus SNP data Added a test for interaction with quantitative traits and a dichotomous covariate Added --merge-list option to merge more than two filesets simultaneously Fixed bug quantitative trait association test (not dealing with missing phenotypes properly) Fixed some minor bugs with parsing the command line V0.96 30-Mar-2006 Fixed bug in --remove option Added Breslow-Day test of homogeneous odds ratios Added option to skip nearby SNPs in case-only epistasis test Added time/date stamps to output Records output in *.log file; most remaining output echoed to STDOUT instead of STDERR (aside from errors and warnings) Improved parsing of command lines (checking numeric inputs, etc) Added -mcc option to specify number of cases:controls in clustering, e.g. for 3:1 matching of cases to controls, for example. V0.95 20-Mar-2006 Added Cochran-Mantel-Haenszel tests (2x2xK and IxJxK) Added homogeneity of odds ratio between clusters test (partitioning chi-square) Added support for gene-dropping simulation V0.94 7-Mar-2006 Added feature to perform error checking of command line options (scan for unused options) Ability to include external matching criteria for --cluster added Ability to specify merge modes and a diff function for PED files V0.93 1-Mar-2006 X chromosome support added for basic association test & quantitative traits Threshold for --genome output based on pi-hat exceeding --min V0.92 22-Feb-2006 X chromosome support added for case/control tests, quantitative trait association, TDT, genotypic correlations, allele frequency statistics. Not yet implemented for the population stratification, inbreeding or epistasis tests. --chr and --from X and --to X options added Some problems with the --merge option corrected Now only considers founders for the allele frequency and HWE tests