picard.vcf

Class LiftoverVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.LiftoverVcf

@DocumentedFeature
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.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALLOW_MISSING_FIELDS_IN_HEADER
static java.lang.String	ATTEMPTED_LOCUS Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
java.io.File	CHAIN
protected static int	EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE
static java.lang.String	FILTER_CANNOT_LIFTOVER_INDEL Filter name to use when a target cannot be lifted over.
static java.lang.String	FILTER_INDEL_STRADDLES_TWO_INTERVALS Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.
static java.lang.String	FILTER_MISMATCHING_REF_ALLELE Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
static java.lang.String	FILTER_NO_TARGET Filter name to use when a target cannot be lifted over.
java.io.File	INPUT
double	LIFTOVER_MIN_MATCH
static java.lang.String	ORIGINAL_CONTIG Attribute used to store the name of the source contig/chromosome prior to liftover.
static java.lang.String	ORIGINAL_START Attribute used to store the position of the variant on the source contig prior to liftover.
java.io.File	OUTPUT
java.io.File	REJECT
boolean	WARN_ON_MISSING_CONTIG
boolean	WRITE_ORIGINAL_POSITION

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
LiftoverVcf()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected static htsjdk.variant.variantcontext.GenotypesContext	fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals, java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> alleleMap)
protected static htsjdk.variant.variantcontext.VariantContext	flipIndel(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.liftover.LiftOver liftOver, htsjdk.samtools.reference.ReferenceSequence referenceSequence)
protected static htsjdk.variant.variantcontext.VariantContext	leftAlignVariant(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.samtools.reference.ReferenceSequence referenceSequence) Normalizes and left aligns a VariantContext.
protected static htsjdk.variant.variantcontext.VariantContext	liftSimpleVariant(htsjdk.variant.variantcontext.VariantContext source, htsjdk.samtools.util.Interval target) liftsOver snps on either positive or negative strand and biallelic indels on positive strand only
static void	main(java.lang.String[] args)
protected ReferenceArgumentCollection	makeReferenceArgumentCollection()

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, 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="The input VCF/BCF file to be lifted over.")
public java.io.File INPUT

OUTPUT

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

CHAIN

@Argument(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 java.io.File CHAIN

REJECT

@Argument(doc="File to which to write rejected records.")
public java.io.File REJECT

WARN_ON_MISSING_CONTIG

@Argument(shortName="WMC",
          doc="Warn on missing contig.",
          optional=true)
public boolean WARN_ON_MISSING_CONTIG

WRITE_ORIGINAL_POSITION

@Argument(doc="Write the original contig/position for lifted variants to the INFO field.",
          optional=true)
public boolean WRITE_ORIGINAL_POSITION

LIFTOVER_MIN_MATCH

@Argument(doc="The minimum percent match required for a variant to be lifted.",
          optional=true)
public double LIFTOVER_MIN_MATCH

ALLOW_MISSING_FIELDS_IN_HEADER

@Argument(doc="Allow INFO and FORMAT in the records that are not found in the header",
          optional=true)
public boolean ALLOW_MISSING_FIELDS_IN_HEADER

EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE

protected static int EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE

FILTER_CANNOT_LIFTOVER_INDEL

public static final java.lang.String FILTER_CANNOT_LIFTOVER_INDEL

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

See Also:

Constant Field Values

FILTER_NO_TARGET

public static final java.lang.String FILTER_NO_TARGET

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

See Also:

Constant Field Values

FILTER_MISMATCHING_REF_ALLELE

public static final java.lang.String FILTER_MISMATCHING_REF_ALLELE

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

See Also:

Constant Field Values

FILTER_INDEL_STRADDLES_TWO_INTERVALS

public static final java.lang.String FILTER_INDEL_STRADDLES_TWO_INTERVALS

Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.

See Also:

Constant Field Values

ORIGINAL_CONTIG

public static final java.lang.String ORIGINAL_CONTIG

Attribute used to store the name of the source contig/chromosome prior to liftover.

See Also:

Constant Field Values

ORIGINAL_START

public static final java.lang.String ORIGINAL_START

Attribute used to store the position of the variant on the source contig prior to liftover.

See Also:

Constant Field Values

ATTEMPTED_LOCUS

public static final java.lang.String ATTEMPTED_LOCUS

Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.

See Also:

Constant Field Values

Constructor Detail

LiftoverVcf

public LiftoverVcf()

Method Detail

makeReferenceArgumentCollection

protected ReferenceArgumentCollection makeReferenceArgumentCollection()

Overrides:

makeReferenceArgumentCollection in class CommandLineProgram

main

public static void main(java.lang.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.

liftSimpleVariant

protected static htsjdk.variant.variantcontext.VariantContext liftSimpleVariant(htsjdk.variant.variantcontext.VariantContext source,
                                                                                htsjdk.samtools.util.Interval target)

liftsOver snps on either positive or negative strand and biallelic indels on positive strand only

Parameters:

source -

target -

Returns:

flipIndel

protected static htsjdk.variant.variantcontext.VariantContext flipIndel(htsjdk.variant.variantcontext.VariantContext source,
                                                                        htsjdk.samtools.liftover.LiftOver liftOver,
                                                                        htsjdk.samtools.reference.ReferenceSequence referenceSequence)

Parameters:

source - original variant context

liftOver - the LiftOver object to use for flipping

referenceSequence - the reference sequence of the target

Returns:

a flipped variant-context.

fixGenotypes

protected static htsjdk.variant.variantcontext.GenotypesContext fixGenotypes(htsjdk.variant.variantcontext.GenotypesContext originals,
                                                                             java.util.Map<htsjdk.variant.variantcontext.Allele,htsjdk.variant.variantcontext.Allele> alleleMap)

leftAlignVariant

protected static htsjdk.variant.variantcontext.VariantContext leftAlignVariant(htsjdk.variant.variantcontext.VariantContext vc,
                                                                               htsjdk.samtools.reference.ReferenceSequence referenceSequence)

Normalizes and left aligns a VariantContext. Based on Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015) Unified Representation of Genetic Variants. Bioinformatics.

Parameters:

vc - the VariantContext to be normalized

referenceSequence - the ReferenceSequence of the same contig as vc

Returns:

a new VariantContext which represents the same variation as vc but has been normalized and left-aligned