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Program : fcGENE
Version: 1.0.7
Aims :
1.To perform snp-wise and individual-wise quality control.
2.To convert plink format data (with or without excluding
low-quality SNPs) to any imputation tool and then to convert back
the imputation results into different formats.
3.To generate templates of imputation command scripts used
by the preferred imputation tool.
4.To filter imputed SNPs by using a threshold of different
imputation quality measures.
5.To convert imputation results of any imputation tools:
(MaCH, IMPUTE, BEAGLE, BIMBAM) into input files of software like:
SNPTEST, HAPLOVIEW, EIGENSOFT and GenABEL,
-VCF,
-genotype data with count of allele
-genotype data with allele-dose
6.To transform genotype data from the format of one imputation tool
to another.
7.To convert imputation-reference panel into plink formatted
genotyped SNP data and other formats and to calculate quality measures.
8.To perform data management like: merging and splitting of two or more than two genotype
data, and exclusion of SNPs and individuals.
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Copyright: GNU General Public License
Program Developer:
Nab Raj Roshyara
Universitaet Leipzig
Leipzig Research Center for Civilization Diseases(LIFE)
Institute for Medical Informatics, Statistics and
Epidemiology (IMISE)
group: Genetical Statistics and Systems Biology
Group Leader: Prof.Dr. Markus Scholz
Contact Email: markus.scholz@imise.uni-leipzig.de
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Use of pre-compiled version of the program:
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1. To use in Windows system:
*-> Download from
http://sourceforge.net/projects/fcgene/files/fcgene-1.0.7.tar.gz/download
and and decompress to get fcgene-1.0.7 directory.
*-> Open command promt (cmd.exe).
*->Go the directory of fcgene-1.0.7 with command ``cd fcgene-1.0.7''.
*-> copy the from fcgene.exe to your working directopy with command
"cp fcgene.exe working_directory"
and start to use fcgene.exe program
2. To use in Linux system:
*->Open Linux console.
*->Use the following command to download:
wget http://sourceforge.net/projects/fcgene/files/fcgene-1.0.7.tar.gz/download
*->To unpack use command : ``tar -zxvf fcgene-1.0.7.tar.gz''.
*->Go the directory of fcgene-1.0.7 with command ``cd fcgene-1.0.7''.
*->If you want to use static version of the program, type command :
``mv fcgene\_static fcgene'',
*->For the dynamic version type command: ``mv fcgene\_dynamic fcgene''.
#############################
Compilation of the program:
#############################
1. Download the latest version of fcGENE and its pdf documentation file.
2. For Linux users:
*->Open Linux console
*->Use the following command to download:
wget http://sourceforge.net/projects/fcgene/files/fcgene-1.0.7.tar.gz/download
*->To unpack use command : ``tar -zxvf fcgene-1.0.7.tar.gz''.
*->Go the directory of fcgene-1.0.7 with command ``cd fcgene-1.0.7''.
*->Execute the commands:
1. ./configure #(type `` ./configure'' and press <enter>).
2. make #(type `` make'' and press <enter>).
3. sudo make install
#( If you want to install the program in your system)
4. fcgene
5. make clean #(To delete *.o files and *gch files from folder src)
*-> If you don't want to install, you can copy ``fcgene'' from src folder to your working directory using
``cp src/fcgene working\_directoy/.''.
*->Start using fcGENE commands as mentioned in fcGENE-documentation file.
*->If you get a problem(something like error: cannot find install-sh or install.sh in
)when using command "./configure", then excute the command:
"automake --add-missing --copy".
while using this command, you may get error but don't worry.
The necessary script "install-sh" script is already created. Now type again
"./configure", "make" , "sudo make install" and finally "fcgene" .
(If you dont have automake program, this can be installed with the command
"apt-get install automake".)
3. For Windows users:
*->Download and install MINGW program from http://www.mingw.org/,
if this is not installed on your computer.
*->Open mSys console installed together with MINGW program
*-> Download and decompress fcgene-1.0.7 from
http://sourceforge.net/projects/fcgene/files/fcgene-1.0.7.tar.gz/download
*->Go the directory of fcgene-1.0.7 with command ``cd fcgene-1.0.7''.
*->Execute the command:
`` ./configure'' (type `` ./configure'' and press enter).
*->Execute the command:
``make'' (type `` make'' and press enter).
Copy ``fcgene'' from src folder to your working directory using
``cp src/fcgene wording\_directoy/.''.
*->Type 'make clean' to delete *.o and *.gch types of files.
*->Start using fcGENE commands as mentioned in fcGENE-documentation file.
is to use fcGENE in "R-commands".
For this put fcgene.exe file in the working directory.
Then you can execute fcGENE by using R-command option:
"system". An example of how to use fcGENE under R, is given below.
system("./fcgene --ped example.ped --map example.map")
4. If you have a compilation error something like:
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
make: *** [fcGENE] Error 1,
then it may be that you do not posses dynamic math-library and/or glibc-dynamic library
which is used for linking c ro c++ files dynamically.
*->The solution is to compile statically
5. If you want that fcGENE reads and writes gezipped file ,then either use
pre-compiled version of fcGENE or make sure that you have zlib library
before you compile and install the program.
6. For static compilation:
Instead of using just "make" in linux command line, type:
make AC_CFLAGS1='-static'
in the linux-command line and <ENTER>.
#Command "make CFLAGS1='-static'" will compile
the program statistically.
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How to start the program
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*->If you have installed fcGENE in your system,then use
``fcgene'' to start the program (without ./ i.e. type ``fcgene'' and <ENTER>).
*->If the program is not installed and you have copied the program
in your current working directory, then use:
``./fcgene''
*->In this manual, I have always used ``./fcgene'' while explaining the different commands of fcGENE.
*->If you have installed the program in your system with sudo make install then
use ``fcgene'' only.
*->``./'' means the executable program ``fcgene'' is contained in the current working directory.
If you don't have executable "fcgene" in your current directory and you use ./fcgene, it won't work.
At such a case just use "fcgene ...".
Remark: Currently I am updating the program very often.Therefore, before using the program,
please look once again at fcGENE's sourceforge homepage if anything is updated.
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