Class SnpSiftCmdGt

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdGt
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdGt extends SnpSift
Add genotype information to INFO fields
Author:
pcingola

  • Field Details

    • SHOW_EVERY

      public static int SHOW_EVERY

  • Constructor Details

    • SnpSiftCmdGt

      public SnpSiftCmdGt()

    • SnpSiftCmdGt

      public SnpSiftCmdGt(String[] args)

  • Method Details

    • getOutput

      public String getOutput()
      Overrides:
      getOutput in class SnpSift

    • headers

      protected List<org.snpeff.vcf.VcfHeaderEntry> headers()
      Description copied from class: SnpSift
      Headers to add
      Overrides:
      headers in class SnpSift

    • parseArgs

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

    • run

      public boolean run()
      Process a VCF entry and return a string (tab separated values)
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift

    • usage

      public void usage(String msg)
      Description copied from class: SnpSift
      Show usage message
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift