Users' documentation for BMapBuilder


Java Runtime Environment

BMapBuilder is a Java 2 program. In order to use it, you need a Java Runtime Environment (JRE) version 1.4 or later. If you do not have it, get and install the newest version of the JRE at: Sun JRE

Java 3D

Since version 2 of BMapBuilder, 3D functionality was added. For 3D functions to be run in your computer you will need to have installed Java 3D, at least version 1.3.1: Download Java3D.
If you perform a manual installation, please make sure files are installed in the correct folder or the program will not start.

Incompatibility notes

It has to be noted that recent versions of Java3D may not be supported by some graphic drivers. If 3D functionality of BMapBuilder 2.0 does not work, you may need either to uninstall Java3D and install and older version (we recommend version 1.3.1 or 1.3.2) or to update your graphic driver.

Download BMapBuilder

Download BMapBuilder 3.2 with 3D functionality (recommended)
Download BMapBuilder 3.1 with 3D functionality
Download BMapBuilder 2.3 with 3D functionality
Download BMapBuilder 2.2 with 3D functionality
Download BMapBuilder 2.1 with 3D functionality
Follow version control

Install BMapBuilder

Windows, Mac OSX

Make sure that the file you have downloaded has extension ".jar", as some Internet browser may change it by ".zip" when downloading. You should be able to start the program by double-clicking on the jar file. The program can also be run by typing java -jar [BMapBuilder jar file] on the command line.

Unix, Linux

The program can be run by typing java -jar BMapBuilder2.jar on the command line or by double-clicking on it.

Large datasets

We recommend to use the argument -Xmx for large datasets. Otherwise the program may return an "out of memory" error. Thus, for large datasets, as chromosome-wide datasets, the program must be run by typing java -jar -XmxMm BMapBuilder2.jar, with M being the maximum internal memory your computer can use in Megabytes. As an example,

java -jar -Xmx2000m BMapBuilder3.1.jar

will allow the program to use a maximum of 2000 MB memory.

Textual user interface

For large data files we strongly recommend to use a textual user interface, as the following example:

java -jar -Xmx2000m BMapBuilder3.1.jar -ng -o=o.png -est=8 -snp1=1 -snp2=4

-Xmx2000m will allow the program to use a maximum of 2000 MB memory
-ng will run the program in textual mode will use file as the input file
-f=o.png will use file o.png as the output file
-est=8 will use information at column 8 as LD measure
-snp1=1 will use column 1 to find the position of SNP 1
-snp2=4 will use column 4 to find the position of SNP 2
Run java -jar BMapBuilder -ng for more information about program arguments.

Input file format

Text files with at least three columns, no matters the order, are required. Each row contains information for a pair of SNPs.
The three columns correspond to the physical position of each SNP in the pair and the estimation value (which must be a value in the interval [0,1]).
Besides these three columns, the program can also uses the major allele relative frequency for each SNP in the pair, i.e., two more columns. The order is not important as the program allows the user to choose the colums.
Other columns in the file will not be taken into account.
Here there is a very small file than can be used as an example of an input file.
There can be a first line in the row with the heading. The number of words in the heading must be the same as columns in the file. Words must be separated by tab, blank space or comma.

Output file format

The bitmap will be written in a png graphic file.
For each snp pair, a square with res bits side will be used to represent the value of the estimation, following this scale:

The value of res can be chosen in the program as well as the color tones (green, red or blue).
We do not recommend resolutions greater than 5 for large files, as those at the International HapMap Project website.

How to use BMapBuilder

In order to build a new 2D/3D bitmap using the Graphical User Inteface (GUI), you have to use the option "Build" in the "2D/3D" menu.
Besides providing a source file, the following mandatory parameters will be required to the user when a 2D bitmap is going to be built, either from the GUI or from the command line: The following parameters are optional:


Please, cite BMapBuilder with the following paper:

Abad-Grau, M.M.; Montes, R.; Sebastiani, P.
"Building chromosome-wide LD maps",
Bioinformatics 22(16): 1933-1934 (2006)

Additional information

Some datasets
Other supplementary information