picard.vcf

Class SplitVcfs

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.SplitVcfs

public class SplitVcfs
extends CommandLineProgram

Splits the input VCF file into two, one for indels and one for SNPs. The headers of the two output files will be identical.

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.io.File	INDEL_OUTPUT
java.io.File	INPUT
java.io.File	SEQUENCE_DICTIONARY
java.io.File	SNP_OUTPUT
java.lang.Boolean	STRICT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SplitVcfs()

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, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

INPUT

@Option(shortName="I",
        doc="The VCF or BCF input file")
public java.io.File INPUT

SNP_OUTPUT

@Option(doc="The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.")
public java.io.File SNP_OUTPUT

INDEL_OUTPUT

@Option(doc="The VCF or BCF file to which indel records should be written. The file format is determined by file extension.")
public java.io.File INDEL_OUTPUT

SEQUENCE_DICTIONARY

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

STRICT

@Option(doc="If true an exception will be thrown if an event type other than SNP or indel is encountered")
public java.lang.Boolean STRICT

Constructor Detail

SplitVcfs

public SplitVcfs()

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.