VCF2SQL

Motivation

Generate the SQL code to insert a VCF into sqlite3. http://www.sqlite.org/

Compilation

See also Compilation

ant vcf2sql

Options

Option	Description
IN=File	VCF files to process. This option may be specified 0 or more times.
SUFFIX=String	Table suffix Default value: (empty).
USE_VEP=Boolean	Use and explode VEP predictions Default value: true. Possible values: {true, false}
USE_SNPEFF=Boolean	Use and explode SNPEFF predictions Default value: true. Possible values: {true, false}
ENGINE=String	sql engine [sqlite,hsql] Default value: sqlite. This option can be set to 'null' to clear the default value.
SPLIT4=Boolean	Split DP4 Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}

Examples

java -jar dist/vcf2sql.jar I=file.vcf | sqlite3 db.sqlite 

Database schema

See also

• VCF2XML