de.charite.compbio.jannovar.cmd.annotate_vcf

Class AnnotateVCFCommand

java.lang.Object

de.charite.compbio.jannovar.cmd.JannovarCommand

de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand

de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand

public class AnnotateVCFCommand
extends JannovarAnnotationCommand

Run annotation steps (read in VCF, write out VCF or Jannovar file format).

Author:

Manuel Holtgrewe, Max Schubach

Constructor Summary

Constructors

Constructor and Description
AnnotateVCFCommand(String[] argv)

Method Summary

Modifier and Type	Method and Description
void	run() This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file with the suffix .de.charite.compbio.jannovar).

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AnnotateVCFCommand

public AnnotateVCFCommand(String[] argv)
                   throws CommandLineParsingException,
                          HelpRequestedException

Throws:

CommandLineParsingException

HelpRequestedException

Method Detail

run

public void run()
         throws JannovarException

This function inputs a VCF file, and prints the annotated version thereof to a file (name of the original file with the suffix .de.charite.compbio.jannovar).

Specified by:

run in class JannovarCommand

Throws:

JannovarException - on problems with the annotation