使用命令：java -jar Haploview.jar -n -h即可获得帮助文件

-h, -help                       Print this message

-v, -version                    Print out the version number

-memory <memsize>               allocates <memsize> megabytes of memory (default 512M内存设定)

-n, -nogui                      Command line output only（命令行模式）

-q, -quiet                      Quiet mode- doesnt print any warnings or information to screen

-log <filename>                 Specify a logfile name (defaults to haploview.log if no name specified)

-out <fileroot>                 Specify a fileroot to be used for all output files

-pedfile <pedfile>              Specify an input file (or http:// location) in pedigree file format

-hapmap <hapmapfile>            Specify an input file (or http:// location) in HapMap format

-phasedhmpdata <phasedfile>     Specify a HapMap PHASE data file (or http:// location)

-phasedhmpsample <samplefile>   Specify a HapMap PHASE sample file (or http:// location)

-phasedhmplegend <legendfile>   Specify a HapMap PHASE legend file (or http:// location)

-gzip                           Indicates that phased input files use GZIP compression

-hapmapDownload                 Specify a phased HapMap download

-haps <hapsfile>                Specify an input file (or http:// location) in .haps format

-info <infofile>                Specify a marker info file (or http:// location)

-plink <plinkfile>              Specify a PLINK or other results file (or http:// location)

-map <mapfile>                  Specify a map file or binary map file (or http:// location)

-nonSNP                         Specify that the accompanying PLINK file is non-SNP based output

-selectCols                     Activate the preloading column filter for PLINK loads

-batch <batchfile>              Batch mode. Each line in batch file should contain a genotype file

                               followed by an optional info file, separated by a space.

-blocks <blockfile>             Blocks file (or http:// location), one block per line, will force output for these blocks

-track <trackfile>              Specify an input analysis track file (or http:// location)

-excludeMarkers <markers>       Specify markers (in range 1-N where N is total number of markers) to be

                               skipped for all analyses. Format: 1,2,5..12

-skipcheck                      Skips the various genotype file checks

-chromosome <1-22,X,Y>          Specifies the chromosome for this file or download

-panel <CEU,YRI,CHB+JPT>        Specifies the analysis panel for this HapMap download

-startpos <integer>             Specifies the start position in kb for this HapMap download

-endpos <integer>               Specifies the end position in kb for this HapMap download

-release <16a,21,22>            Specifies the HapMap phase for this HapMap download (defaults to 21)

-dprime                         Outputs LD text to <fileroot>.LD

-png                            Outputs LD display to <fileroot>.LD.PNG

-compressedpng                  Outputs compressed LD display to <fileroot>.LD.PNG

-svg                            Outputs svg format LD display to <fileroot>.LD.SVG

-infoTrack                      Downloads and displays HapMap info track on PNG image output

-ldcolorscheme <argument>       Specify an LD color scheme. <argument> should be one of:

                               DEFAULT, RSQ, DPALT, GAB, GAM

-ldvalues <DPRIME,RSQ,NONE>     Specify what to print in LD image output. default is DPrime

-check                          Outputs marker checks to <fileroot>.CHECK

                               note: -dprime  and -check default to no blocks output.

                               Use -blockoutput to also output blocks

-indcheck                       Outputs genotype percent per individual to <fileroot>.INDCHECK

-mendel                         Outputs Mendel error information to <fileroot>.MENDEL

-malehets                       Outputs male heterozygote information to <fileroot>.MALEHETS

-blockoutput <GAB,GAM,SPI,ALL>  Output type. Gabriel, 4 gamete, spine output or all 3. default is Gabriel.

-blockCutHighCI <thresh>        Gabriel 'Strong LD' high confidence interval D' cutoff.

-blockCutLowCI <thresh>         Gabriel 'Strong LD' low confidence interval D' cutoff.

-blockMAFThresh <thresh>        Gabriel MAF threshold.

-blockRecHighCI <thresh>        Gabriel recombination high confidence interval D' cutoff.

-blockInformFrac <thresh>       Gabriel fraction of informative markers required to be in LD.

-block4GamCut <thresh>          4 Gamete block cutoff for frequency of 4th pairwise haplotype.

-blockSpineDP <thresh>          Solid Spine blocks D' cutoff for 'Strong LD

-maxdistance <distance>         Maximum comparison distance in kilobases (integer). （默认500kb)

-hapthresh <frequency>          Only output haps with at least this frequency

-spacing <threshold>            Proportional spacing of markers in LD display. <threshold> is a value

                               between 0 (no spacing) and 1 (max spacing). Default is 0

-minMAF <threshold>             Minimum minor allele frequency to include a marker. <threshold> is a value

                               between 0 and 0.5. (Default is 0.001)

-maxMendel <integer>            Markers with more than <integer> Mendel errors will be excluded. Default is 1.

-minGeno <threshold>            Exclude markers with less than <threshold> valid data. <threshold> is a value

                               between 0 and 1. Default is .75

-hwcutoff <threshold>           Exclude markers with a HW p-value smaller than <threshold>. <threshold> is a value

                               between 0 and 1. (Default is 0.001)

-missingCutoff <threshold>      Exclude individuals with more than <threshold> fraction missing data.

                               <threshold> is a value between 0 and 1. Default is .5

-assocCC                        Outputs case control association results to <fileroot>.ASSOC and <fileroot>.HAPASSOC

-assocTDT                       Outputs trio association results to <fileroot>.ASSOC and <fileroot>.HAPASSOC

-customAssoc <file>             Loads a set of custom tests for association.

-permtests <numtests>           Performs <numtests> permutations on default association tests (or custom tests

                               if a custom association file is specified) and writes to <fileroot>.PERMUT

-pairwiseTagging                Generates pairwise tagging information in <fileroot>.TAGS and .TESTS

-aggressiveTagging              As above but generates 2-marker haplotype tags unless specified otherwise by -aggressiveNumMarkers

-aggressiveNumMarkers <2,3>     Specifies whether to use 2-marker haplotype tags or 2 and 3-marker haplotype tags.

-maxNumTags <n>                 Only selects <n> best tags.

-dontaddtags                    Only uses forced in tags.

-includeTags <markers>          Forces in a comma separated list of marker names as tags.

-includeTagsFile <file>         Forces in a file (or http:// location) of one marker name per line as tags.

-excludeTags <markers>          Excludes a comma separated list of marker names from being used as tags.

-excludeTagsFile <file>         Excludes a file (or http:// location) of one marker name per line from being used as tags.

-captureAlleles <file>          Capture only the alleles contained in a file (or http:// location) of one marker name per line.

-designScores <file>            Specify design scores in a file (or http:// location) of one marker name and one score per line

-mindesignscores <threshold>    Specify a minimum design score threshold.

-mintagdistance <distance>      Specify a Minimum distance in bases between picked tags.

-taglodcutoff <thresh>          Tagger LOD cutoff for creating multimarker tag haplotypes.

-tagrsqcutoff <thresh>          Tagger r^2 cutoff.