HapMapUtil

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Contents

Introduction

HapMapUtil (HMU) is a set of programs allowing to handle genotype data in the HapMap format. More specifically, the HMUgeno program is able to filter samples and genetic variants from HapMap data before formatting them for eQTNMiner, BimBam or IMPUTE2.


Installation

You can retrieve the code of HapMapUtil using CVS (see Download). Once it is done, enter into the directory and run ./autogen.sh.

Then, if you want to install the library for everyone on your machine, you need to log as root or to execute all the following commands via sudo:

$ ./configure
$ make clean
$ make
$ make install

If you are not root, you can precise the path to the directory in which you want the library to be installed:

$ ./configure --prefix=<path_to_directory>

where <path_to_directory> is $HOME/src/HapMapUtil/ for instance.

Finally, you can add the path to the bin directory to your environment:

$ HMU=$HOME/src/HapMapUtil
$ export PATH=$HMU/bin:$PATH

You may want to add these lines to your .bash_profile and source it:

$ . ~/.bash_profile


Examples

The program named HMUgeno is usually the most useful. It takes as input a configuration file which template is available in the repository (file HMUgeno_config.txt). As usual, a description is available in command-line:

$ HMUgeno --help
HMUgeno - version 1.0

Copyright (C) 2008-2009  Jean-Baptiste Veyrieras (University of Chicago)
HMUgeno comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.

* These options set a flag:
--help	Display a brief help on program usage
--verbose	Output message on standard output to see what the program is doing
--no-gzip	Raw data files are not gzipped

* These options require arguments:
--config or -c	The configuration file
--output or -o	The output directory
--format or -f	The output format (eqtnminer/bimbam/impute2)
--pop or -p	The population name
--release or -r	The release number
--build or -b	The build number
--hapmap-dir or -h	The HapMap directory containing the raw data files
--chromosome or -m	The specific chromosome to extract

Here is an example of the configuration file:

$ cat HMUgeno_config.txt
Release 28
BuildNumber 36
FileStemPattern genotypes_<chromosome>_<pop>_r<release>_nr.b<build>_fwd.txt
SNPOutFile list_YRI_variant_IDs_to_ignore.txt
SampleInFile samples_YRI.txt
HapMapPath /data/share/HapMap/genotypes/r28/2010-08_phaseII+III/forward

where the file list_YRI_variant_IDs_to_ignore.txt contains SNPs to ignore, and where the file samples_YRI.txt contains samples to extract.

Th program can now be launched:

$ HMUgeno -c HMUgeno_config.txt -p YRI -o YRI_b36_eqmr/ -f eqtnminer --verbose


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