Package picard.util
Class LiftOverIntervalList
java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.LiftOverIntervalList
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 a Picard interval_list file as an input. See
IntervalListTools
documentation for information on
interval_list format. Note: for lifting over VCF files use LiftoverVcf tool.
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 ofMIN_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
FieldsModifier and TypeFieldDescriptiondouble
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
OUTPUT
-
SEQUENCE_DICTIONARY
@Argument(doc="Sequence dictionary to place in the output interval list. (This should be any file from which the dictionary of the target reference can be extracted.)", shortName="SD") public File SEQUENCE_DICTIONARY -
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 File REJECT
-
-
Constructor Details
-
LiftOverIntervalList
public LiftOverIntervalList()
-
-
Method Details
-
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 classCommandLineProgram
- Returns:
- program exit status.
-