picard.util

Class LiftOverIntervalList

java.lang.Object

picard.cmdline.CommandLineProgram

picard.util.LiftOverIntervalList

@DocumentedFeature
public class LiftOverIntervalList
extends CommandLineProgram

This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references. It is based on the UCSC LiftOver tool and uses a UCSC chain file to guide its operation. It accepts both Picard interval_list files or VCF files as interval inputs.

Usage example:

 java -jar picard.jar LiftOverIntervalList \
       I=input.interval_list \
       O=output.interval_list \
       SD=reference_sequence.dict \
       CHAIN=build.chain
 

Return codes

If all the intervals lifted over successfully, program will return 0. It will return 1 otherwise.

Caveats

An interval is "lifted" in its entirety, but it might intersect (a "hit") with multiple chain-blocks. Instead of placing the interval in multiple hits, it is lifted over using the first hit that passes the threshold of MIN_LIFTOVER_PCT. For large enough MIN_LIFTOVER_PCT this is non-ambiguous, but if one uses small values of MIN_LIFTOVER_PCT (perhaps in order to increase the rate of successful hits...) the liftover could end up going to the smaller of two good hits. On the other hand, if none of the hits pass the threshold a warning will be emitted and the interval will not be lifted.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	CHAIN
java.io.File	INPUT
double	MIN_LIFTOVER_PCT
java.io.File	OUTPUT
java.io.File	REJECT
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
LiftOverIntervalList()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

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(doc="The input interval list to be lifted over.",
          shortName="I")
public java.io.File INPUT

OUTPUT

@Argument(doc="The output interval list file.",
          shortName="O")
public java.io.File OUTPUT

SEQUENCE_DICTIONARY

@Argument(doc="Sequence dictionary to place in the output interval list. (This should be the dictionary of the target reference.)",
          shortName="SD")
public java.io.File SEQUENCE_DICTIONARY

CHAIN

@Argument(doc="Chain file that guides the LiftOver process.")
public java.io.File CHAIN

MIN_LIFTOVER_PCT

@Argument(doc="Minimum percentage of bases in each input interval that must map to output interval for liftover of that interval to occur. If the program fails to find a good target for an interval, a warning will be emitted and the interval will be dropped from the output. ")
public double MIN_LIFTOVER_PCT

REJECT

@Argument(doc="Interval List file for intervals that were rejected",
          optional=true)
public java.io.File REJECT

Constructor Detail

LiftOverIntervalList

public LiftOverIntervalList()

Method Detail

doWork

protected int doWork()

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.