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
Transform a VCF to a TPED file
- Author:
- pcingola
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Nested Class Summary
Nested Classes -
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
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Constructor Summary
Constructors -
Method Summary
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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Constructor Details
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SnpSiftCmdVcf2Tped
public SnpSiftCmdVcf2Tped() -
SnpSiftCmdVcf2Tped
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Method Details
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init
public void init()Default parameters -
parseArgs
Description copied from class:SnpSift
Parse command line arguments -
run
public boolean run()Run annotations -
usage
Show usage message -
vcf2Tped
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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