jvarkit

VcfToSql

Generate the SQL code to insert a VCF into mysql

Usage

Usage: vcf2sql [options] Files
  Options:
    -d, --drop
      Add Drop Tables Statement
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -f, --nofilter
      ignore FILTER column
      Default: false
    -n, --noinfo
      ignore INFO column
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -s, --schema
      Print Schema
      Default: false
    --version
      print version and exit

Keywords

• vcf
• sql

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2sql

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcf2sql/VcfToSql.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcf2sql/VcfToSqlTest.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite vcf2sql ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Examples

java -jar dist/vcf2sql.jar  file.vcf | mysql -u user -p -D vcf_db 

Database schema (dot)

digraph G{
vcffile;
sample;
sample2file;
allele;
filter;
chromosome;
variant;
variant2alt;
variant2filter;
vepPrediction;
vepPrediction2so;
genotype;
sample2file -> vcffile[label=vcffile_id];
sample2file -> sample[label=sample_id];
filter -> vcffile[label=vcffile_id];
chromosome -> vcffile[label=vcffile_id];
variant -> vcffile[label=vcffile_id];
variant -> chromosome[label=chromosome_id];
variant -> allele[label=ref_id];
variant2alt -> variant[label=variant_id];
variant2alt -> allele[label=alt_id];
variant2filter -> variant[label=variant_id];
variant2filter -> filter[label=filter_id];
vepPrediction -> variant[label=variant_id];
vepPrediction2so -> vepPrediction[label=vepPrediction_id];
genotype -> variant[label=variant_id];
genotype -> sample[label=sample_id];
genotype -> allele[label=a1_id];
genotype -> allele[label=a2_id];
}

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