picard.vcf

Class MergeVcfs

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.MergeVcfs

@DocumentedFeature
public class MergeVcfs
extends CommandLineProgram

Combines multiple VCF files into a single file. Input files must be sorted by their contigs and, within contigs, by start position. Throws IllegalArgumentException if the contig lists are not present in the input files, are not identical or if the sample lists are not the same; this class uses the GATK to merge headers, which may throw exceptions if the headers cannot be merged. See VCFUtils.smartMergeHeaders for details.

An index file is created for the output file by default. Using an output file name with a ".gz" extension will create gzip-compressed output.

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.io.File>	INPUT
java.io.File	OUTPUT
java.io.File	SEQUENCE_DICTIONARY

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
MergeVcfs()

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

INPUT

@Argument(shortName="I",
          doc="VCF or BCF input files (File format is determined by file extension), or a file having a \'.list\' suffix containing the path to the files.",
          minElements=1)
public java.util.List<java.io.File> INPUT

OUTPUT

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

SEQUENCE_DICTIONARY

@Argument(shortName="D",
          doc="The index sequence dictionary to use instead of the sequence dictionary in the input file",
          optional=true)
public java.io.File SEQUENCE_DICTIONARY

Constructor Detail

MergeVcfs

public MergeVcfs()

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.