picard.vcf

Class MakeSitesOnlyVcf

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 and Description
java.io.File	INPUT
java.io.File	OUTPUT
java.util.Set<java.lang.String>	SAMPLE

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

Constructor Summary

Constructors

Constructor and Description
MakeSitesOnlyVcf()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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 java.io.File INPUT

OUTPUT

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

SAMPLE

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

Constructor Detail

MakeSitesOnlyVcf

public MakeSitesOnlyVcf()

Method Detail

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.