Package org.snpsift

Class SnpSiftCmdVcf2Tped

java.lang.Object
org.snpsift.SnpSift
org.snpsift.SnpSiftCmdVcf2Tped
All Implemented Interfaces:
org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator

public class SnpSiftCmdVcf2Tped extends SnpSift
Transform a VCF to a TPED file
Author:
pcingola
  • Constructor Details

    • SnpSiftCmdVcf2Tped

      public SnpSiftCmdVcf2Tped()
    • SnpSiftCmdVcf2Tped

      public SnpSiftCmdVcf2Tped(String[] args)
  • Method Details

    • init

      public void init()
      Default parameters
      Overrides:
      init in class SnpSift
    • 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()
      Run annotations
      Specified by:
      run in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      run in class SnpSift
    • usage

      public void usage(String msg)
      Show usage message
      Specified by:
      usage in interface org.snpeff.snpEffect.commandLine.CommandLine
      Overrides:
      usage in class SnpSift
      Parameters:
      msg -
    • vcf2Tped

      public void vcf2Tped(String vcfFile, String tfamFile, String outTfamFile, String outTpedFile)
      Convert a VCF to a TPED file
      Parameters:
      vcfFile -
      tpedFile - Important: If the variant is NOT a SNP, we create a 'fake' snp ( A -> T ). This is done in order to be able to MAP InDels into PED files and keep compatibility with downstream programs (GenAble). Yes, it's an awful hack. YOu've been warned!