Chapter 3. Command Line Options

Haploview can be run from the command li ne without the display in order to do processing of multiple datasets or quick computation on very large datasets. In order to run Haploview without the display, add the "-nogui" flag. The "-help" flag shows a condensed explanation of all the command line options explained below.

General Options

-h, -help

Print help information.

-n, -nogui

Command line mode—does not launch display.

-q, -quiet

Quiet mode—minimizes output to command line.

Input Options

-pedfile <filename>

Specify a genotype input file in pedigree format. This option works in GUI mode.

-hapmap <filename>

Specify a HapMap format input file. This option works in GUI mode.

-haps <filename>

Specify a phased input file. This option works in GUI mode.

-info <filename>

Specify a marker information file. This option works in GUI mode.

-batch <filename>

Specify a batch load file.

-blocks <filename>

Specify a block definition file. This will automatically use this block definition for haplotype output.

-track <filename>

Specify an analysis track file

Data Check Options

-skipcheck

Skip all the genotype data quality checks and uses all markers for all analyses.

-minMAF <threshold>

Exclude all markers with minor allele frequency below <threshold>, which must be between 0 and 0.5. Default of 0. This option works in GUI mode.

-maxMendel <integer>

Exclude markers with greater than <integer> Mendelian inheritance errors. Default of 1. This option works in GUI mode.

-minGeno <threshold>

Exclude markers with less than <threshold> fraction of nonzero genotypes. <threshold> must be between 0 and 1 with a default of 0.5. This option works in GUI mode.

-hwcutoff <threshold>

Exclude markers with a Hardy Weinberg p-value less than <threshold>, which ranges from 0 to 1 with a default of 0.001 This option works in GUI mode.

-maxDistance <distance>

Maximum intermarker distance for LD comparisons (in kilobases). Default is 500. This option works in GUI mode.

-missingCutoff <threshold>

Exclude individuals with more than <threshold> fraction missing data, where <threshold> is a value between 0 and 1 with a default of 0.5. This option works in GUI mode.

Output Options

-blockoutput <type>

Generate haplotypes and population frequencies for blocks of <type>, which can be GAB (Gabriel et al), GAM (4 gamete blocks), SPI (solid spine blocks) or ALL (each of the previous 3). The default block type is Gabriel. More information can be found with the blocks help.

-check

Output marker quality checks to <inputfile>.CHECK

-dprime

Output pairwise LD text table to <inputfile>.LD. Note that -dprime and -check default to no haplotype output unless the -blockoutput flag is also specified.

-png

Output PNG image file of LD display to <inputfile>.LD.PNG

-compressedpng

Output low-resolution (smaller file) PNG image of LD display to <inputfile>.LD.PNG

-spacing <threshold>

Use proportional spacing for dumped LD pngs. <threshold> ranges from 0 (no spacing) to 1 (max spacing) with a default of 0.

-ldcolorscheme <type>

Use a particular color scheme for dumped LD pngs. <type> can be DEFAULT, RSQ, DPALT, GAB or GAM. More information can be found with the LD display help

-assocCC

Output case/control association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results are not generated if block type is set to ALL.

-assocTDT

Output TDT association results. Saves single marker results to <inputfile>.ASSOC and haplotype results to <inputfile>.HAPASSOC. Haplotype association results not generated if block type is set to ALL.

-hapthresh <threshold>

Only output haplotypes with frequency ≥ <threshold>. Note that multiallelic D' and htSNPs are computed using only displayed haplotypes.

-excludeMarkers <markers>

Exclude markers in a comma separated list with ranges specified as start..end. So, to exclude markers 3, 5 and 10 through 15 you'd use "-excludeMarkers 3,5,10..15"