MakeSitesOnlyVcf (picard 2.18.2 API)

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

```
@DocumentedFeature
public class MakeSitesOnlyVcf
extends CommandLineProgram
```
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
Summary
This tool reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information, including annotations based on genotypes (e.g. AN, AF). Output can be any supported variant format including .vcf, .vcf.gz or .bcf.
Inputs
- Input VCF or BCF file containing genotype and site-level information.
- Output VCF or BCF file containing only site-level information.
- [Optional] Names of one or more samples to include in the output VCF.
Usage example:
```
     java -jar picard.jar MakeSitesOnlyVcf \
      INPUT=input_variants.vcf \
      OUTPUT=output_variants.vcf
 
```

Field Summary

Fields
Modifier and Type Field Description

File INPUT

File OUTPUT

Set<String> SAMPLE
- 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`
`File`	`OUTPUT`
`Set<String>`	`SAMPLE`

Constructor Summary

Constructors
Constructor Description

MakeSitesOnlyVcf()

Constructors
Constructor	Description
`MakeSitesOnlyVcf()`

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 VCF or BCF containing genotype and site-level information.")
public File INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output VCF or BCF file containing only site-level information.")
public File OUTPUT

SAMPLE

@Argument(shortName="S",
          doc="Names of one or more samples to include in the output VCF.",
          optional=true)
public Set<String> SAMPLE

Constructor Detail
- MakeSitesOnlyVcf
```
public MakeSitesOnlyVcf()
```

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 MakeSitesOnlyVcf

Summary

Inputs

Usage example:

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

SAMPLE

Constructor Detail

MakeSitesOnlyVcf

Method Detail

main

doWork