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

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

SnpSiftCmdVcf2Tped.UseMissing
Field Summary

Fields inherited from class SnpSift
args, BUILD, command, config, configFile, dataDir, dbFileName, dbTabix, dbType, debug, download, EMPTY_ARGS, errCount, genomeVersion, help, log, needsConfig, needsDb, needsGenome, numWorkers, output, quiet, REVISION, saveOutput, shiftArgs, SHOW_EVERY_VCFLINES, showVcfHeader, showVersion, SOFTWARE_NAME, suppressOutput, vcfHeaderAddProgramVersion, vcfHeaderProcessed, vcfInputFile, verbose, VERSION, VERSION_MAJOR, VERSION_NO_NAME, VERSION_SHORT
Constructor Summary

Constructors

Constructor

Description

SnpSiftCmdVcf2Tped()

SnpSiftCmdVcf2Tped(String[] args)
Method Summary

Modifier and Type

Method

Description

void

init()

Default parameters

void

parseArgs(String[] args)

Parse command line arguments

boolean

run()

Run annotations

void

usage(String msg)

Show usage message

void

vcf2Tped(String vcfFile, String tfamFile, String outTfamFile, String outTpedFile)

Convert a VCF to a TPED file

Methods inherited from class SnpSift
addHeaders, annotate, annotateFinish, annotateInit, cmd, commandLineStr, databaseDownload, databaseFind, error, getArgs, getConfig, getConfigFile, getOutput, headers, isOpt, loadConfig, main, openVcfInputFile, processVcfHeader, setCommand, setCommand, setConfig, setConfigFile, setDbFileName, setDebug, setQuiet, setSaveOutput, setShowVcfHeader, setShowVersion, setSuppressOutput, setVcfHeaderAddProgramVersion, setVerbose, showCmd, showVersion, unSanitize, usageGenericAndDb

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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!

Class SnpSiftCmdVcf2Tped

Nested Class Summary

Field Summary

Fields inherited from class SnpSift

Constructor Summary

Method Summary

Methods inherited from class SnpSift

Methods inherited from class Object

Constructor Details

SnpSiftCmdVcf2Tped

SnpSiftCmdVcf2Tped

Method Details

init

parseArgs

run

usage

vcf2Tped