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LiftOverIntervalList (Picard)

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 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.

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 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.

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
null Chain file that guides the LiftOver process.
--INPUT
 -I
null The input interval list to be lifted over.
--OUTPUT
 -O
null The output interval list file.
--SEQUENCE_DICTIONARY
 -SD
null Sequence dictionary to place in the output interval list. (This should be the dictionary of the target reference.)
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
null 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 a BAM index when writing a coordinate-sorted BAM file.
--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
null 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 / NA

read one or more arguments files and add them to the command line

List[File]  []


--CHAIN / NA

Chain file that guides the LiftOver process.

R File  null


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false


--CREATE_MD5_FILE / NA

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false


--GA4GH_CLIENT_SECRETS / NA

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 / NA

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 / NA

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 / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--REJECT / NA

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 the dictionary of the target reference.)

R File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

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 / NA

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 / NA

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 / NA

display the version number for this tool

boolean  false


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GATK version 4.1.4.0 built at Wed, 9 Oct 2019 15:19:59 -0400.