Package org.snpsift
Class SnpSiftCmdVcf2Tped
- java.lang.Object
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- org.snpsift.SnpSift
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- org.snpsift.SnpSiftCmdVcf2Tped
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SnpSiftCmdVcf2Tped.UseMissing
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description SnpSiftCmdVcf2Tped()
SnpSiftCmdVcf2Tped(java.lang.String[] args)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
init()
Default parametersvoid
parseArgs(java.lang.String[] args)
Parse command line argumentsboolean
run()
Run annotationsvoid
usage(java.lang.String msg)
Show usage messagevoid
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
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Method Detail
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parseArgs
public void parseArgs(java.lang.String[] args)
Description copied from class:SnpSift
Parse command line arguments
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run
public boolean run()
Run annotations
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usage
public void usage(java.lang.String msg)
Show usage message
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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!
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