RAREMETAL DOWNLOAD & BUILD

Useful Wiki Pages

• The RAREMETALWORKER documentation
• The RAREMETAL documentation
• The FAQ
• The Change Log

Where to Download

• University of Michigan CSG users can go to the following:

 /net/wonderland/home/saichen/Raremetal/

GIT HUB

Please clone or download from GitHub:

https://github.com/statgen/Raremetal

There is a known issue with the newest versions (>=4.14.0) of RAREMETAL, which may give incorrect p-values for some burden test calculation methods. We are working on a fix, but for now we recommend using an older version (<= 4.13.9).

Since v4.13.6, MAC and WINDOWS version are no longer updated. Please download old versions from here:

• for MAC OS X

• for Windows/CygWin64

• for Windows/MinGW

From version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package.

SCRIPTS

Calculating Odds Ratio from RAREMETALWORKER output

• If you want to estimate Odds Ratios of variants analyzed by RAREMETALWORKER, the script calculateOddsRatio.pl can help you augment RAREMETALWORKER output with estimated odds ratio to the last column.
• The script can also be found in the RAREMETAL package 4.13.6 and later, under directory raremetal/script/calculateOddsRatio.pl.

How to Compile

• gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to GNU gfortran for download.

• If you prefer to build from scratch, then do the following in your Raremetal directory:

 prompt> make clean
 prompt> make
 #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. 

• If you prefer to build individual tool:

 prompt> cd Raremetal/raremetalworker/
 prompt> make
 #This will build RAREMETALWORKER under raremetal/bin/ directory.

 prompt> cd Raremetal/raremetal/
 prompt> make
 #This will build RAREMETAL under raremetal/bin/ directory.

• If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to openMP.

 prompt> cd raremetalworker/src
 prompt> make openmp
 #This will build RAREMETALWORKER under raremetal/bin/ directory.

• If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.

FAQ

For compiling questions, please go to FAQ for more information.

OLD VERSIONS

(All linux versions)

• v4.13.8
• v4.13.6