Running Subtraction program in Command line mode:

For CMD mode use the following command:
$ tmc-snp
Usage: tmc-snp [options]

-h, --help  show this help message and exit
-i               Input tumor VCF file (required)
-o              Output file after TMC-SNPdb subtraction (Optional)
-l             Load a custom normal variations database (with tmc-snp schema - refer README/ SCHEMA document in the package). Give SQLITE file as input (Optional)
--vcf_dir   Directory path containing VCF files containing germline variants. Required for
--sql         Output germline variant database. Required for creating custom database.

*use the help option
tmc-snp -h
tmc-snp --help

Subtraction of user tumor vcf against TMC-SNPdb.
*To subtract germline variants from tumor VCF using TMC-SNPdb, use the command (without specifying output file name).
tmc-snp –i input.vcf –o output.vcf (Optional)

Create a custom germline database:
User can create their own germline database with a set of normal/germline variant VCF files.
The following command can be used;

$ tmc-snp --vcf-dir directory/path/to/vcf --sql output.sqlite

The output SQLite file is created with the following schema:
chr       - holds chromosome number data, e.g. 'chr2'
pos      - integer storing the position on the chromosome, e.g. 190023
orig      - reference base as found in the reference genome, e.g. 'A'
change- altered base found in the samples, e.g. 'T'
reccur  - recurrence of a particular change (A->T as in the above example) in across samples

Schema to create a custom database
Following is sql syntax could be used to create custom sqlite database file format

( "chr" TEXT,
"pos" INTEGER,
"orig" TEXT,
"change" TEXT,
"reccur" INTEGER

Output from this program can be loaded for subtraction from tumor samples using the '-l' option
of the program.
For example:
$ tmc-snp -i tumor.vcf -l custom_database.sql