GLMVC was developed using C# language under Microsoft Windows. The software can be run under command prompt window at Windows system with .Net framework 4.0+ installed. It can also be run under linux or Mac OS X with a runtime environment named mono installed.

[mono] (http://www.mono-project.com/)

For Mac OS X user, you may download and install mono from mono project

For linux user, you may want to download and install mono source code as following. The mono will be installed into "/scratch/cqs/shengq1/mono/" and you may change it to where you want. The "make" command may take a few minutes.

git clone git://github.com/mono/mono.git
cd mono
./autogen.sh --prefix=/scratch/cqs/shengq1/mono --enable-btls=no 
make
make install

You may also need to set up environment variable PATH

export PATH=/scratch/cqs/shengq1/mono/bin:$PATH

After re-login into system, you can validate the installation using following command:

mono --version

Mono JIT compiler version 3.4.1 (master/69a1519 Fri May  9 11:58:21 CDT 2014)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
    TLS:           __thread
    SIGSEGV:       altstack
    Notifications: epoll
    Architecture:  amd64
    Disabled:      none
    Misc:          softdebug
    LLVM:          supported, not enabled.
    GC:            sgen

[samtools] (http://samtools.sourceforge.net/) for pileup

Old version of samtools may not generate base position in read correctly. samtools version 1.1+ is highly recommended.

[R] (http://www.r-project.org/) for filter

brglm and stringr packages are required.

#after you start R, install brglm and stringr packages
install.packages(c("brglm","stringr"))

[annovar] (https://doc-openbio.readthedocs.io/projects/annovar/en/latest/) for annotation

In order to use table_annovar.pl, you need to download required databases using following script:

#assume that you have already put annovar directory into your path
mkdir humandb
annotate_variation.pl -buildver hg19 -downdb gene humandb/
annotate_variation.pl -buildver hg19 -downdb segdup humandb/
annotate_variation.pl -buildver hg19 -downdb 1000g2012apr humandb/
annotate_variation.pl -buildver hg19 -downdb snp138 humandb/
annotate_variation.pl -downdb -webfrom annovar -buildver hg19 avsift humandb/
annotate_variation.pl -downdb -webfrom annovar -buildver hg19 ljb_all humandb/
annotate_variation.pl -downdb -webfrom annovar -buildver hg19 esp6500si_all humandb/
cd humandb
wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/phastConsElements46way.txt.gz
gunzip phastConsElements46way.txt.gz
mv phastConsElements46way.txt hg19_phastConsElements46way.txt
cd ..