Haploview 4.2 Command line options
-h, -help                       Print this message
-v, -version                    Print out the version number
-memory <memsize>               allocates <memsize> megabytes of memory (default 512)
-n, -nogui                      Command line output only
-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