Package org.snpsift

Class SnpSiftCmdRemoveReferenceGenotypes

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdRemoveReferenceGenotypes extends SnpSift
Removes reference genotypes. I.e. replaces the genotype string by the MISSING string ('.') if the genotype is just homozygous reference (e.g. '0/0')
Author:
pablocingolani
  • Field Details

  • Constructor Details

    • SnpSiftCmdRemoveReferenceGenotypes

      public SnpSiftCmdRemoveReferenceGenotypes()
    • SnpSiftCmdRemoveReferenceGenotypes

      public SnpSiftCmdRemoveReferenceGenotypes(String[] args)
  • Method Details

    • parseArgs

      public void parseArgs(String[] args)
      Description copied from class: SnpSift
      Parse command line arguments
      Specified by:
      parseArgs in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      parseArgs in class SnpSift
    • run

      public boolean run()
      Analyze the file
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
    • usage

      public void usage(String errMsg)
      Show usage and exit
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift