Lifts over an interval list from one reference build to another. 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 (see: http://genome.ucsc.edu/cgi-bin/hgLiftOver) 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.chainReturn 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.Category Intervals Manipulation
Overview
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 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.LiftOverIntervalList (Picard) specific arguments
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Arguments | |||
--CHAIN |
Chain file that guides the LiftOver process. | ||
--INPUT -I |
The input interval list to be lifted over. | ||
--OUTPUT -O |
The output interval list file. | ||
--SEQUENCE_DICTIONARY -SD |
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.) | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--help -h |
false | display the help message | |
--MIN_LIFTOVER_PCT |
0.95 | 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. | |
--REJECT |
Interval List file for intervals that were rejected | ||
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
--CREATE_INDEX |
false | Whether to create an index when writing VCF or coordinate sorted BAM output. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
--TMP_DIR |
One or more directories with space available to be used by this program for temporary storage of working files | ||
--USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
--USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
--VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--VERBOSITY |
INFO | Control verbosity of logging. | |
Advanced Arguments | |||
--showHidden |
false | display hidden arguments |
Argument details
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--CHAIN
Chain file that guides the LiftOver process.
R File null
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INPUT / -I
The input interval list to be lifted over.
R File null
--MAX_RECORDS_IN_RAM
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--MIN_LIFTOVER_PCT
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.
double 0.95 [ [ -∞ ∞ ] ]
--OUTPUT / -O
The output interval list file.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--REJECT
Interval List file for intervals that were rejected
File null
--SEQUENCE_DICTIONARY / -SD
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.)
R File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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