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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SnpSiftCmdVcf2Tped.UseMissing

Field Summary

Fields inherited from class org.snpsift.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(java.lang.String[] args)

Method Summary

Modifier and Type	Method	Description
void	init()	Default parameters
void	parseArgs(java.lang.String[] args)	Parse command line arguments
boolean	run()	Run annotations
void	usage(java.lang.String msg)	Show usage message
void	vcf2Tped(java.lang.String vcfFile, java.lang.String tfamFile, java.lang.String outTfamFile, java.lang.String outTpedFile)	Convert a VCF to a TPED file

Methods inherited from class org.snpsift.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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SnpSiftCmdVcf2Tped

public SnpSiftCmdVcf2Tped()

SnpSiftCmdVcf2Tped

public SnpSiftCmdVcf2Tped(java.lang.String[] args)

Method Detail

init

public void init()

Default parameters

Overrides:

init in class SnpSift

parseArgs

public void parseArgs(java.lang.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(java.lang.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(java.lang.String vcfFile,
                     java.lang.String tfamFile,
                     java.lang.String outTfamFile,
                     java.lang.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!