Package org.snpsift

Class SnpSiftCmdConcordance

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdConcordance
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator
public class SnpSiftCmdConcordance extends SnpSift
Calculate genotyping concordance between two VCF files. Typical usage: Calculate concordance between sequencing experiment and genotypting experiment.
Author:
pcingola

  • Field Details

  • Constructor Details

    • SnpSiftCmdConcordance

      public SnpSiftCmdConcordance()

    • SnpSiftCmdConcordance

      public SnpSiftCmdConcordance(String[] args)

  • Method Details

    • getConcordance

      public org.snpeff.stats.CountByType getConcordance()

    • getConcordanceBySample

      public org.snpeff.collections.AutoHashMap<String,org.snpeff.stats.CountByType> getConcordanceBySample()

    • getCountEntries

      public int getCountEntries()

    • init

      public void init()
      Description copied from class: SnpSift
      Initialize default values
      Overrides:
      init 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()
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift

    • setWriteBySampleFile

      public void setWriteBySampleFile(boolean writeBySampleFile)

    • setWriteSummaryFile

      public void setWriteSummaryFile(boolean writeSummaryFile)

    • usage

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