Verify mate-pair information between mates and fix if needed.This tool ensures that all mate-pair information is in sync between each read and its mate pair. If no OUTPUT file is supplied then the output is written to a temporary file and then copied over the INPUT file (with the original placed in a .old file.) Reads marked with the secondary alignment flag are written to the output file unchanged. However supplementary reads are corrected so that they point to the primary, non-supplemental mate record.
Usage example
java -jar picard.jar FixMateInformation \ I=input.bam \ O=fixed_mate.bam \ ADD_MATE_CIGAR=trueCaveats
The program should run with fairly limited memory unless there are many mate pairs that are missing or far apart from each other in the file, as it keeps track of the unmatched mates.Category Read Data Manipulation
Overview
Summary
This tool ensures that all mate-pair information is in sync between each read and its mate pair. If no #OUTPUT file is supplied then the output is written to a temporary file and then copied over the #INPUT file (with the original placed in a .old file.) Reads marked with the secondary alignment flag are written to the output file unchanged. However, supplementary reads are corrected so that they point to the primary, non-supplemental mate record.Usage example:
java -jar picard.jar FixMateInformation \ I=input.bam \ O=fixed_mate.bam \ ADD_MATE_CIGAR=true
Caveats
The program should run with fairly limited memory unless there are many mate pairs that are missing or far apart from each other in the file, as it keeps track of the unmatched matesFixMateInformation (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 files to check and fix. Multiple files will be merged and sorted. | |
Optional Tool Arguments | |||
--ADD_MATE_CIGAR -MC |
true | Adds the mate CIGAR tag (MC) if true, does not if false. | |
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--ASSUME_SORTED -AS |
false | If true, assume that the input file is queryname sorted, even if the header says otherwise. | |
--help -h |
false | display the help message | |
--IGNORE_MISSING_MATES |
true | If true, ignore missing mates, otherwise will throw an exception when missing mates are found. | |
--OUTPUT -O |
null | The output file to write to. If no output file is supplied, the input file is overwritten (only available with single input file). | |
--SORT_ORDER -SO |
null | Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. | |
--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.
--ADD_MATE_CIGAR / -MC
Adds the mate CIGAR tag (MC) if true, does not if false.
Boolean true
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--ASSUME_SORTED / -AS
If true, assume that the input file is queryname sorted, even if the header says otherwise.
boolean false
--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
--IGNORE_MISSING_MATES / NA
If true, ignore missing mates, otherwise will throw an exception when missing mates are found.
Boolean true
--INPUT / -I
The input files to check and fix. Multiple files will be merged and sorted.
R List[File] []
--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 [ [ -∞ ∞ ] ]
--OUTPUT / -O
The output file to write to. If no output file is supplied, the input file is overwritten (only available with single input file).
File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--SORT_ORDER / -SO
Optional sort order if the OUTPUT file should be sorted differently than the INPUT file.
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 / 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
GATK version 4.0.5.2 built at 25-50-2019 01:50:01.
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