RenameSampleInVcf (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.vcf.RenameSampleInVcf

```
@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.

Field Summary

Fields
Modifier and Type Field Description

File INPUT

String NEW_SAMPLE_NAME

String OLD_SAMPLE_NAME

File OUTPUT
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Fields
Modifier and Type	Field	Description
`File`	`INPUT`
`String`	`NEW_SAMPLE_NAME`
`String`	`OLD_SAMPLE_NAME`
`File`	`OUTPUT`

Constructor Summary

Constructors
Constructor Description

RenameSampleInVcf()

Constructors
Constructor	Description
`RenameSampleInVcf()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.
`static void`	`main(String[] args)`

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

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

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input single sample VCF or BCF file.")
public File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output single sample VCF.")
public File OUTPUT

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

NEW_SAMPLE_NAME

@Argument(doc="New name to give sample in output VCF.")
public String NEW_SAMPLE_NAME

Constructor Detail
- RenameSampleInVcf
```
public RenameSampleInVcf()
```

Method Detail
- main
```
public static void main(String[] args)
```
- 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 class CommandLineProgram
  
  Returns:
  
  program exit status.

Class RenameSampleInVcf

Summary

Inputs

Usage example:

Notes

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

INPUT

OUTPUT

OLD_SAMPLE_NAME

NEW_SAMPLE_NAME

Constructor Detail

RenameSampleInVcf

Method Detail

main

doWork