picard.vcf

Class LiftoverVcf

java.lang.Object

picard.cmdline.CommandLineProgram

picard.vcf.LiftoverVcf

@DocumentedFeature
public class LiftoverVcf
extends CommandLineProgram

Summary

Tool for "lifting over" a VCF from one genome build to another, producing a properly headered, sorted and indexed VCF in one go.

Details

This tool adjusts the coordinates of variants within a VCF file to match a new reference. The output file will be sorted and indexed using the target reference build. To be clear, CommandLineProgram.REFERENCE_SEQUENCE should be the target reference build (that is, the "new" one). The tool is based on the UCSC LiftOver tool and uses a UCSC chain file to guide its operation.
For each variant, the tool will look for the target coordinate, reverse-complement and left-align the variant if needed, and, in the case that the reference and alternate alleles of a SNP have been swapped in the new genome build, it will adjust the SNP, and correct AF-like INFO fields and the relevant genotypes.

Example

 java -jar picard.jar LiftoverVcf \\
     I=input.vcf \\
     O=lifted_over.vcf \\
     CHAIN=b37tohg38.chain \\
     REJECT=rejected_variants.vcf \\
     R=reference_sequence.fasta
 

Caveats

Rejected Records

Records may be rejected because they cannot be lifted over or because of sequence incompatibilities between the source and target reference genomes. Rejected records will be emitted to the REJECT file using the source genome build coordinates. The reason for the rejection will be stated in the FILTER field, and more detail may be placed in the INFO field.

Memory Use

LiftOverVcf sorts the output using a SortingCollection which relies on CommandLineProgram.MAX_RECORDS_IN_RAM to specify how many (vcf) records to hold in memory before "spilling" to disk. The default value is reasonable when sorting SAM files, but not for VCFs as there is no good default due to the dependence on the number of samples and amount of information in the INFO and FORMAT fields. Consider lowering to 100,000 or even less if you have many genotypes.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ALLOW_MISSING_FIELDS_IN_HEADER
static java.lang.String	ATTEMPTED_ALLELES Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
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
boolean	DISABLE_SORT
static int	EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE
static java.lang.String	FILTER_CANNOT_LIFTOVER_REV_COMP 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
boolean	LOG_FAILED_INTERVALS
static java.lang.String	ORIGINAL_ALLELES Attribute used to store the list of original alleles (including REF), in the original order prior to liftover.
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
boolean	RECOVER_SWAPPED_REF_ALT
java.io.File	REJECT
java.util.Collection<java.lang.String>	TAGS_TO_DROP
java.util.Collection<java.lang.String>	TAGS_TO_REVERSE
boolean	WARN_ON_MISSING_CONTIG
boolean	WRITE_ORIGINAL_ALLELES
boolean	WRITE_ORIGINAL_POSITION

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, 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 ReferenceArgumentCollection	makeReferenceArgumentCollection()

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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 for the lifted over VCF/BCF.")
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

LOG_FAILED_INTERVALS

@Argument(shortName="LFI",
          doc="If true, intervals failing due to match below LIFTOVER_MIN_MATCH will be logged as a warning to the console.",
          optional=true)
public boolean LOG_FAILED_INTERVALS

WRITE_ORIGINAL_POSITION

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

WRITE_ORIGINAL_ALLELES

@Argument(doc="Write the original alleles for lifted variants to the INFO field.  If the alleles are identical, this attribute will be omitted.",
          optional=true)
public boolean WRITE_ORIGINAL_ALLELES

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

RECOVER_SWAPPED_REF_ALT

@Argument(doc="If the REF allele of the lifted site does not match the target genome, that variant is normally rejected. For bi-allelic SNPs, if this is set to true and the ALT allele equals the new REF allele, the REF and ALT alleles will be swapped.  This can rescue some variants; however, do this carefully as some annotations may become invalid, such as any that are alelle-specifc.  See also TAGS_TO_REVERSE and TAGS_TO_DROP.",
          optional=true)
public boolean RECOVER_SWAPPED_REF_ALT

TAGS_TO_REVERSE

@Argument(doc="INFO field annotations that behave like an Allele Frequency and should be transformed with x->1-x when swapping reference with variant alleles.",
          optional=true)
public java.util.Collection<java.lang.String> TAGS_TO_REVERSE

TAGS_TO_DROP

@Argument(doc="INFO field annotations that should be deleted when swapping reference with variant alleles.",
          optional=true)
public java.util.Collection<java.lang.String> TAGS_TO_DROP

DISABLE_SORT

@Argument(doc="Output VCF file will be written on the fly but it won\'t be sorted and indexed.",
          optional=true)
public boolean DISABLE_SORT

EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE

public static int EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE

FILTER_CANNOT_LIFTOVER_REV_COMP

public static final java.lang.String FILTER_CANNOT_LIFTOVER_REV_COMP

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

ORIGINAL_ALLELES

public static final java.lang.String ORIGINAL_ALLELES

Attribute used to store the list of original alleles (including REF), in the original order 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

ATTEMPTED_ALLELES

public static final java.lang.String ATTEMPTED_ALLELES

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

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.