Chapter 3 - Command Line Options

Haploview can be run from the command line with or without the normal display window. Sometimes due to memory constraints, or familiarity of the user the normal interface is slower and more cumbersome than the command line. In order to do processing of multiple datasets or quick computation on very large datasets we recommend that you become familiar with the command line arguments that Haploview accepts.

If you are unfarmiliar with what a terminal or command line is, we suggest that you first become familiar with one. You should be comfortable with general navigation as well as moving/deleting/creating files and folders. If you use Windows start here, if you use OS X or if you use Unix start here.

Haploview can be launched from your terminal using:

java -jar Haploview.jar

If you wish to run Haploview strictly from the terminal, you must disable the GUI - or graphical user interface - like so:


java -jar Haploview.jar  -nogui 



If you wish to see the major command line arguments, without this website, invoke Haploview like this:

java -jar Haploview.jar  -nogui -help



Here is an example of a command that will download Hapmap data from chromosome 11 from the Yoruban Panel:

java -jar Haploview.jar -n -hapmapDownload -chromosome 11 -startpos 22508 -endpos 22515 -panel YRI -blockoutput ALL -release 22



If you come across an argument that requires extra input from you, you will see something like this:

-chromosome <chrom#>; -startpos <start# in kb>; -panel <PanelName>



The < > indicates where you must enter your parameters, leaving this blank will keep the program from functioning as intended.