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FixMateInformation (Picard)

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=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 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 mates

FixMateInformation (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


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GATK version 4.1.2.0 built at Tue, 23 Apr 2019 14:55:55 -0400.