Dependencies:
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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 (http://www.sqlite.org/download.html)
wget http://www.sqlite.org/sqlite-autoconf-3070603.tar.gz
tar xvfz sqlite-autoconf-3071502.tar.gz
cd sqlite-autoconf-3071502
./configure --prefix=/usr/local
make
sudo make install
Get and Install PyVcf
pyvcf (http://pyvcf.readthedocs.org/en/latest/)
wget https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.7.tar.gz
tar xvfz PyVCF-0.6.7.tar.gz
sudo python setup.py install
Get and Install Python TKinter
python TKinter library for executing the GUI mode
sudo apt-get install python-tk
Installation:
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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:
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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.