VCF4J

Java utility for parsing the variant call format file content

See Variant Call Format Wikipedia

Example

Parsing

 VCFData vcfData = VCFUtils.read()
                           .from(new File("genome.vcf"))
                           .parse();

Parsing and writing

VCFUtils.write(VCFUtils.read()
                       .fromFile("input.vcf")
                       .parseOnce()
                       .filter(record -> record.getInfoValue(AdditionalInfo.CLIN_risk_factor)
                                               .isPresent()))
        .intoFile("output.vcf");

Maven Snapshots

<dependency>
  <groupId>org.omnaest.genomics</groupId>
  <artifactId>VCF4J</artifactId>
  <version>0.0.1-SNAPSHOT</version>
</dependency>

<repositories>
    <repository>
        <id>ossrh</id>
        <url>https://oss.sonatype.org/content/repositories/snapshots</url>
        <snapshots>
            <enabled>true</enabled>
        </snapshots>
    </repository>
</repositories>