Package picard.vcf
Class RenameSampleInVcf
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- picard.cmdline.CommandLineProgram
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- picard.vcf.RenameSampleInVcf
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@DocumentedFeature public class RenameSampleInVcf extends CommandLineProgram
Renames a sample within a VCF or BCF.Summary
This tool enables the user to rename a sample in either a VCF or BCF file. It is intended to change the name of a sample in a VCF prior to merging with VCF files in which one or more samples have similar names. Note that the input VCF file must be single-sample VCF and that the NEW_SAMPLE_NAME argument is required.Inputs
- Input single-sample VCF or BCF file.
- Output single-sample VCF or BCF file.
- New name to give sample in output VCF.
- [Optional] Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name.
Usage example:
java -jar picard.jar RenameSampleInVcf \ INPUT=input_variants.vcf \ OUTPUT=output_variants.vcf \ NEW_SAMPLE_NAME=sample
Notes
The input VCF (or BCF) must be single-sample.
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Field Summary
Fields Modifier and Type Field Description File
INPUT
String
NEW_SAMPLE_NAME
String
OLD_SAMPLE_NAME
File
OUTPUT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description RenameSampleInVcf()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="Input single sample VCF or BCF file.") public File INPUT
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OUTPUT
@Argument(shortName="O", doc="Output single sample VCF.") public File OUTPUT
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OLD_SAMPLE_NAME
@Argument(doc="Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name", optional=true) public String OLD_SAMPLE_NAME
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NEW_SAMPLE_NAME
@Argument(doc="New name to give sample in output VCF.") public String NEW_SAMPLE_NAME
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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