TMC-SNPdb subtraction tool depends on three python libraries sqlite3, Tkinter (for GUI version) and pyvcf (version >= 0.6.7). These libraries can be installed using following commands:

Get and Install sqlite
sqlite3 (
tar xvfz sqlite-autoconf-3071502.tar.gz
cd sqlite-autoconf-3071502
./configure --prefix=/usr/local
sudo make install

Get and Install PyVcf
pyvcf (
tar xvfz PyVCF-0.6.7.tar.gz
sudo python install

Get and Install Python TKinter
python TKinter library for executing the GUI mode
sudo apt-get install python-tk

To install 'tmc-snpdb' on your Linux system, please follow step 1 & 2.
1) Untar TMC-SNPdb package using following command:
  > tar xvf tmc-snpdb1.0.tar.gz
2) Run the INSTALL script (as administrator) on your system
  > chmod +x INSTALL
  > sudo sh INSTALL
3) Subtraction tool runs in two modes, Graphical user interface (GUI) and command line (CMD). Use 'tmc-snpdb' command on the terminal to execute it in CMD mode; Use 'tmc-snpdb-gui' to run 'tmc-snpdb' in GUI mode.

Test Run:
Test VCF files are provided in the "data/test_vcf" directory. This directory contains two files; test1.vcf (227779 variants) and test2.vcf (115884 variants)

Command line mode:
To subtract germline variants from tumor VCF using TMC-SNPdb, use the command
$tmc-snpdb –i data/test_vcf/test1.vcf –o test1_output.vcf
'-o' - output is an option argument
Output file after subtraction from test1_output.vcf and test2_output.vcf will contains 224330 and 114388 variants, respectively.

In GUI mode:
Click on "UPLOAD A VCF FILE", select a file in /data/test_vcf
Directory in the file dialogue box. Then click on "RUN" to subtract variants.

On an Intel-i5-3210M CPU @2.5GHz x 4-32 bit Ubuntu (14.04) system with 8 GB RAM it takes 72 minutes to process test1.vcf and 56 minutes to process test2.vcf.