WHAMM!: Whole-Genome Homozygosity Analysis and Mapping Machina WHAMM...!
Latest WHAMM release is v0.14 (03-Nov-2008)

Whole-Genome Homozygosity Analysis and Mapping Machina

Introduction | Basics | Download | Commands | Usage | Input | Output | Association | Summaries | Permutations | Imputations | FAQ

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. The Model, Usage, and Pipeline 6. Input Files and Formats 7. Output Files and Formats 8. Association Analysis 9. Data Summaries 10. Permutations 11. Integrated Haplotype Score (iHS) Selection Scan 12. Note on Imputated Data

XX. FAQ & Hints


This page contains some important information regarding how to set up and use WHAMM, as well as additional files generally required by the program.


WHAMM is available for free download, though the current version is considered "alpha" with a formal publication currently in progress. As such, be aware that there will be bugs, revisions, and general changes that may happen between now and the time that a version is finalized for publication (and even then, revisions and bug fixed will continue).

Below are links to gunzip (.gz) files containing the WHAMM package. This package is designed primarily for the Linux/Unix operating environment. It is assumed that you have PERL installed, as well as a recent version of R.

Platform File Version
Linux/Unix whamm_v0.14a.tar.gz v0.14a
Linux/Unix whamm_v0.14.tar.gz v0.14
Linux/Unix whamm_v0.13.tar.gz v0.13

Required for the integrated haplotype score (iHS) selection scanning analysis framework is a C executable which tabulates the unstandardized iHS score.

Platform File Version
Linux/Unix iHS_calc_v1.0.1.tar.gz v1.0.1

Additional Files

CentiMorgan Map files [.bim format]:

Affymetrix 5.0 classic [two chip] - Download
Affymetrix 6.0 - [Coming Soon] Download
Illumnia HumanHap 370K [excluding X chromosome] - Download

Hotspot definition file:

Hapmap Phase I+II b35 - Download

Ancestral States definition file:

Hapmap Phase I+II b35 [from the Haplotter website] - Download

Extracting WHAMM

After downloading the program, you will need to decompress and extract the package to use. To do this, use

tar -xzvf whamm.tar.gz

Note that here the exact name of the tarball will depend on the version of the program you are downloading, e.g. "whamm_v0.13.tar.gz" for version v0.13 rather than simply "whamm.tar.gz". Ultimately, these steps will unpack a directory which contains the program executable and associated perl packages and R routines.

WHAMM Installation and General Usage Notes

You should install the package into either the current working directory or somewhere in the command path. If you are not familiar with the concept of the path variable, ask your system administrator to help. In a UNIX/Linux environment, this would mean extracting the package to either




assuming these directories exist and are in the path. To see which directories are in the path, typing


You will then need to set a specific path for the package so that it will look in the subdirectory which you just extracted (i.e., whamm_v0.13). I advise having a system administrator help you with this, though you could try:

mkdir ~/bin/
mv whamm_v0.13/ ~/bin/.
export PATH=$PATH:~/bin/whamm_v0.13

[Note that you could skip the first step if you already have a local bin/ directory that you use]. Once installed and the path is correctly set, you should make sure that the program is working, by using:


at the command line prompt will run WHAMM, no matter which current directory you happen to be in. WHAMM is a command line program - clicking or trying to use a mouse to initiate features will get you nowehere. It might be required that you set the program to an executable, by typing:

chmod +x WHAMM.pl

Though you could forgo changing the script to executable, and called perl directly:

perl WHAMM.pl

though I find this to be slightly less efficient.

iHS Scan Software Setup

In order to utilize the selection scanning framework and toolkit incorporated into WHAMM, the integrated haplotyupe score (iHS) calculation software must be downloaded, compiled, and installed into the WHAMM directory.

The iHS calculation source code (and associated tarball) can be downloaded from the WHAMM website here.

After downloading the program, you will need to move this tarball to the WHAMM working directory and then the package to use. To do this, use

mv iHS_calc.tar.gz $WHAMM_PATH/.

where $WHAMM_PATH is the path of the WHAMM.pl executable. If you are unsure of the path where your WHAMM executable is located, I recommend contacting a network administrator, or looking here for help on installing WHAMM. This command is then followed by:

tar -xzvf iHS_calc.tar.gz

Note that here the exact name of the tarball will depend on the version of the program you are downloading, e.g. "iHS_calc_v1.0.1.tar.gz" for version v1.0 rather than simply "iHS_calc.tar.gz".

Once yout have extracted the tarball, you will need to move into the newly created directory 'iHS_bin' (containing source code) and compile the executable. To do that, use:

cd iHS_bin
make iHS_calc

If the compilation is successful, you can check the compilation by using:


which should return the command line usage as well as version information. If this command is successful, WHAMM should be prepared to use this calculator for iHS scanning.


This document last modified Monday, 02-Apr-2012 17:35:45 EDT