Reverts the original base qualities and adds the mate cigar tag to read-group BAMs.
Category Read Data Manipulation
Overview
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs. If the file does not have OQs and already has mate cigar tags, nothing is done. New BAM/BAI/MD5 files are created.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 file to revert the state of. | ||
--OUTPUT -O |
The output SAM/BAM 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. | |
--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] []
--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
--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 SAM/BAM 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 file to create.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File 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
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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