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

This document last modified Wednesday, 25-Jan-2017 11:39:26 EST