picard.vcf

Class VcfToIntervalList

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.VcfToIntervalList

@DocumentedFeature
public class VcfToIntervalList
extends CommandLineProgram

Converts a VCF or BCF file to a Picard Interval List.

This tool creates a Picard Interval List from a VCF or BCF. It is important that the file extension is included as the file format is determined by the file extension. Variants that were filtered can be included in the output interval list by setting INCLUDE_FILTERED to true.

Inputs

• A BCF or VCF input file
• Boolean if variants that were filtered should be included in the output interval list

Output

A Picard Interval List

Usage example:

     java -jar picard.jar VcfToIntervalList \
          I=input_variants.vcf \
          O=output.interval_list
 

Field Summary

Fields

Modifier and Type	Field and Description
boolean	INCLUDE_FILTERED
static java.lang.String	INCLUDE_FILTERED_SHORT_NAME
java.io.File	INPUT
static htsjdk.samtools.util.Log	LOG
java.io.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

Constructor Summary

Constructors

Constructor and Description
VcfToIntervalList()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] argv)

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

INCLUDE_FILTERED_SHORT_NAME

public static final java.lang.String INCLUDE_FILTERED_SHORT_NAME

See Also:

Constant Field Values

LOG

public static final htsjdk.samtools.util.Log LOG

INPUT

@Argument(doc="The BCF or VCF input file. The file format is determined by file extension.",
          shortName="I")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="The output Picard Interval List.")
public java.io.File OUTPUT

INCLUDE_FILTERED

@Argument(shortName="IF",
          doc="Include variants that were filtered in the output interval list.",
          optional=true)
public boolean INCLUDE_FILTERED

Constructor Detail

VcfToIntervalList

public VcfToIntervalList()

Method Detail

main

public static void main(java.lang.String[] argv)

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.