Class SnpSiftCmdHwe

java.lang.Object
org.snpsift.SnpSift
org.snpsift.hwe.SnpSiftCmdHwe
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdHwe extends SnpSift
Calculate Hardy-Weinberg equilibrium and goodness of fit for each entry in a VCF file
Author:
pablocingolani

  • Field Details

  • Constructor Details

    • SnpSiftCmdHwe

      public SnpSiftCmdHwe()

    • SnpSiftCmdHwe

      public SnpSiftCmdHwe(String[] args)

  • Method Details

    • main

      public static void main(String[] args)
      Main

    • 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()
      Analyze the file (run multi-thread mode)
      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