TMC-SNPdb 2.0 database and toolkit

TMC-SNPdb 2.0 (an updated version of TMC-SNPdb), wherein we report 305,132 unique variants of Indian origin from 173 in-house normal samples. We have shown utility of ethnic specific resources in somatic analysis hence we have incorporated other databases like IndiGenomes [2], GenomeAsia 100K [3] in our toolkit to create/combine/annotate from custom germline databases in vcf format.

Getting Started

Pre-requisites required for installation of TMC-SNPdb 2.0 toolkit

TMC-SNPdb 2.0 toolkit is developed using python3 and R shiny package.

System Prerequisites:

• Conda

With the following system prerequisites in place, users can use the following commands in the Linux / Unix environment to install the required python packages.

Installation

TMCSNPdb 2.0 can be downloaded from this webpage. Untar the downloaded tar.gz file using the following command:

tar -xvzf tmcsnpdb2tk.tar.gz
cd tmcsnpdb2tk

Make sure that the complete 'untarred' data directory is present in the tmcsnpdb2tk home directory before proceeding with the further installation and running tmcsnpdb2tk. In the home directory of tmcsnpdb2tk (TMCSNPdb 2.0), run the following command:

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conda env create -f tmcsnpdb2tkenv.yml

This installs all the dependencies and tools required to run TMCSNPdb 2.0.

For running any script pertaining to TMCSNPdb 2.0, make sure that the tmcsnpdbtk Conda environment is activated. More information about Conda environments can be found here