Running Subtraction program in Command line mode:
For CMD mode use the following command:
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$ tmc-snp
Usage: tmc-snp [options]
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.
Example:
*use the help option
tmc-snp -h
or
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:
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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
CREATE TABLE tmcsnpdb
( "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