RevertOriginalBaseQualitiesAndAddMateCigar (Picard)

Reverts the original base qualities and adds the mate cigar tag to read-group files.

Category Read Data Manipulation

Overview

This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files. If the file does not have OQs and already has mate cigar tags, nothing is done. New BAM/BAI/MD5 files are created. @author Nils Homer

RevertOriginalBaseQualitiesAndAddMateCigar (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
--INPUT -I		The input SAM/BAM/CRAM file to revert the state of.
--OUTPUT -O		The output SAM/BAM/CRAM file to create.
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
--MAX_RECORDS_TO_EXAMINE	10000	The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file.
--RESTORE_ORIGINAL_QUALITIES -OQ	true	True to restore original qualities from the OQ field to the QUAL field if available.
--SORT_ORDER -SO		The sort order to create the reverted output file with.By default, the sort order will be the same as the input.
--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	true	Whether to create an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	true	Whether to create an MD5 digest for any BAM or FASTQ files created.
--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] []

--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 true

--CREATE_MD5_FILE

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

boolean true

--help / -h

display the help message

boolean false

--INPUT / -I

The input SAM/BAM/CRAM file to revert the state of.

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 [ [ -∞ ∞ ] ]

--MAX_RECORDS_TO_EXAMINE

The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file.

int 10000 [ [ -∞ ∞ ] ]

--OUTPUT / -O

The output SAM/BAM/CRAM file to create.

R File null

--QUIET

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath null

--RESTORE_ORIGINAL_QUALITIES / -OQ

True to restore original qualities from the OQ field to the QUAL field if available.

boolean true

--showHidden / -showHidden

display hidden arguments

boolean false

--SORT_ORDER / -SO

The sort order to create the reverted output file with.By default, the sort order will be the same as the input.

The --SORT_ORDER argument is an enumerated type (SortOrder), which can have one of the following values:

unsorted
queryname
coordinate
duplicate
unknown

SortOrder null

--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

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.