picard.vcf

Class LiftoverVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.LiftoverVcf

public class LiftoverVcf
extends CommandLineProgram

Tool for lifting over a VCF to another genome build and producing a properly header'd, sorted and indexed VCF in one go.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
File	CHAIN
static String	FILTER_CANNOT_LIFTOVER Filter name to use when a target cannot be lifted over.
static String	FILTER_MISMATCHING_REF_ALLELE Filter name to use when a target is lifted over, but the reference allele doens't match the new reference.
File	INPUT
File	OUTPUT
File	REFERENCE_SEQUENCE
File	REJECT

Fields inherited from class picard.cmdline.CommandLineProgram

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

Constructor Summary

Constructors

Constructor and Description
LiftoverVcf()

Method Summary

Methods

Modifier and Type	Method and 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, 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 input VCF/BCF file to be lifted over.")
public File INPUT

OUTPUT

@Option(shortName="O",
        doc="The output location to write the lifted over VCF/BCF to.")
public File OUTPUT

CHAIN

@Option(shortName="C",
        doc="The liftover chain file. See https://genome.ucsc.edu/goldenPath/help/chain.html for a description of chain files.  See http://hgdownload.soe.ucsc.edu/downloads.html#terms for where to download chain files.")
public File CHAIN

REJECT

@Option(doc="File to which to write rejected records.")
public File REJECT

REFERENCE_SEQUENCE

@Option(shortName="R",
        common=false,
        doc="The reference sequence (fasta) for the TARGET genome build.  The fasta file must have an accompanying sqeuence dictionary (.dict file).")
public File REFERENCE_SEQUENCE

FILTER_CANNOT_LIFTOVER

public static final String FILTER_CANNOT_LIFTOVER

Filter name to use when a target cannot be lifted over.

See Also:

Constant Field Values

FILTER_MISMATCHING_REF_ALLELE

public static final String FILTER_MISMATCHING_REF_ALLELE

Filter name to use when a target is lifted over, but the reference allele doens't match the new reference.

See Also:

Constant Field Values

Constructor Detail

LiftoverVcf

public LiftoverVcf()

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.