This tool takes in a coordinate-sorted SAM or BAM and calculatesthe NM, MD, and UQ tags by comparing with the reference.
This may be needed when MergeBamAlignment was run with SORT_ORDER other than 'coordinate' and thuscould not fix these tags then. The input must be coordinate sorted in order to run. If specified,the MD and NM tags can be ignored and only the UQ tag be set.

Usage example:

java -jar picard.jar SetNmMdAndUqTags 
      R=reference_sequence.fasta 
      I=sorted.bam 
      O=fixed.bam 

Category Read Data Manipulation

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Overview

Fixes the NM, MD, and UQ tags in a SAM or BAM file.

This tool takes in a coordinate-sorted SAM or BAM file and calculates the NM, MD, and UQ tags by comparing with the reference.

This may be needed when MergeBamAlignment was run with SORT_ORDER other than 'coordinate' and thus could not fix these tags then. The input must be coordinate sorted in order to run. If specified, the MD and NM tags can be ignored and only the UQ tag be set.

Inputs

The BAM or SAM file to fix

A reference sequence

Output

A BAM or SAM output file with recalculated NM, MD, and UQ tags

Usage example:

Fix the tags in a BAM file:

     java -jar picard.jar SetNmMdAndUqTags \
          R=reference_sequence.fasta \
          I=sorted.bam \
          O=fixed.bam
 

SetNmMdAndUqTags (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	null	The BAM or SAM file to fix.
--OUTPUT  -O	null	The fixed BAM or SAM output file.
--REFERENCE_SEQUENCE  -R	null	Reference sequence file.
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
--IS_BISULFITE_SEQUENCE	false	Whether the file contains bisulfite sequence (used when calculating the NM tag).
--SET_ONLY_UQ	false	Only set the UQ tag, ignore MD and NM.
--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.
--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.

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--arguments_file / NA

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

List[File]  []

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--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX / NA

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

Boolean  false

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--CREATE_MD5_FILE / NA

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

boolean  false

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--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json

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--help / -h

display the help message

boolean  false

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--INPUT / -I

The BAM or SAM file to fix.

R File  null

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--IS_BISULFITE_SEQUENCE / NA

Whether the file contains bisulfite sequence (used when calculating the NM tag).

boolean  false

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--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  [ [ -∞  ∞ ] ]

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--OUTPUT / -O

The fixed BAM or SAM output file.

R File  null

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--QUIET / NA

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

Boolean  false

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

R File  null

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--SET_ONLY_UQ / NA

Only set the UQ tag, ignore MD and NM.

boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []

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--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false

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--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false

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--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

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--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

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.0.6.0 built at 25-39-2019 01:39:46.