Validates a SAM or BAM file.

This tool reports on the validity of a SAM or BAM file relative to the SAM format specification. This is useful for troubleshooting errors encountered with other tools that may be caused by improper formatting, faulty alignments, incorrect flag values, etc.

By default, the tool runs in VERBOSE mode and will exit after finding 100 errors and output them to the console (stdout). Therefore, it is often more practical to run this tool initially using the MODE=SUMMARY option. This mode outputs a summary table listing the numbers of all 'errors' and 'warnings'.

When fixing errors in your file, it is often useful to prioritize the severe validation errors and ignore the errors/warnings of lesser concern. This can be done using the IGNORE and/or IGNORE_WARNINGS arguments. For helpful suggestions on error prioritization, please follow this link to obtain additional documentation on ValidateSamFile.

After identifying and fixing your 'warnings/errors', we recommend that you rerun this tool to validate your SAM/BAM file prior to proceeding with your downstream analysis. This will verify that all problems in your file have been addressed.

Usage example:

java -jar picard.jar ValidateSamFile \
      I=input.bam \
      MODE=SUMMARY

To obtain a complete list with descriptions of both 'ERROR' and 'WARNING' messages, please see our additional documentation for this tool.

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Return codes depend on the errors/warnings discovered:

-1 failed to complete execution 0 ran successfully 1 warnings but no errors 2 errors and warnings 3 errors but no warnings

Category Diagnostics and Quality Control

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Overview

This tool reports on the validity of a SAM or BAM file relative to the SAM format specification. This is useful for troubleshooting errors encountered with other tools that may be caused by improper formatting, faulty alignments, incorrect flag values, etc.

By default, the tool runs in VERBOSE mode and will exit after finding 100 errors and output them to the console (stdout). Therefore, it is often more practical to run this tool initially using the MODE=SUMMARY option. This mode outputs a summary table listing the numbers of all 'errors' and 'warnings'.

When fixing errors in your file, it is often useful to prioritize the severe validation errors and ignore the errors/warnings of lesser concern. This can be done using the IGNORE and/or IGNORE_WARNINGS arguments. For helpful suggestions on error prioritization, please follow this link to obtain additional documentation on ValidateSamFile.

After identifying and fixing your 'warnings/errors', we recommend that you rerun this tool to validate your SAM/BAM file prior to proceeding with your downstream analysis. This will verify that all problems in your file have been addressed.

This tool is a wrapper for SamFileValidator.

Usage example:

 java -jar picard.jar ValidateSamFile \\

       I=input.bam \\

       MODE=SUMMARY
 

To obtain a complete list with descriptions of both 'ERROR' and 'WARNING' messages, please see our additional documentation for this tool.

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ValidateSamFile (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	Input SAM/BAM 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
--IGNORE	[]	List of validation error types to ignore.
--IGNORE_WARNINGS	false	If true, only report errors and ignore warnings.
--INDEX_VALIDATION_STRINGENCY	EXHAUSTIVE	If set to anything other than IndexValidationStringency.NONE and input is a BAM file with an index file, also validates the index at the specified stringency. Until VALIDATE_INDEX is retired, VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.
--IS_BISULFITE_SEQUENCED  -BISULFITE	false	Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as an error in computing the value of the NM tag.
--MAX_OPEN_TEMP_FILES	8000	Relevant for a coordinate-sorted file containing read pairs only. Maximum number of file handles to keep open when spilling mate info to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the 'ulimit -n' command on a Unix system.
--MAX_OUTPUT  -MO	100	The maximum number of lines output in verbose mode
--MODE  -M	VERBOSE	Mode of output
--OUTPUT  -O	null	Output file or standard out if missing
--SKIP_MATE_VALIDATION  -SMV	false	If true, this tool will not attempt to validate mate information. In general cases, this option should not be used. However, in cases where samples have very high duplication or chimerism rates (> 10%), the mate validation process often requires extremely large amounts of memory to run, so this flag allows you to forego that check.
--VALIDATE_INDEX	true	DEPRECATED. Use INDEX_VALIDATION_STRINGENCY instead. If true and input is a BAM file with an index file, also validates the index. Until this parameter is retired VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.
--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.

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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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--IGNORE / NA

List of validation error types to ignore.

List[Type]  []

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--IGNORE_WARNINGS / NA

If true, only report errors and ignore warnings.

boolean  false

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--INDEX_VALIDATION_STRINGENCY / NA

If set to anything other than IndexValidationStringency.NONE and input is a BAM file with an index file, also validates the index at the specified stringency. Until VALIDATE_INDEX is retired, VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.

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

EXHAUSTIVE

LESS_EXHAUSTIVE

NONE

IndexValidationStringency  EXHAUSTIVE

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--INPUT / -I

Input SAM/BAM file

R File  null

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--IS_BISULFITE_SEQUENCED / -BISULFITE

Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as an error in computing the value of the NM tag.

boolean  false

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--MAX_OPEN_TEMP_FILES / NA

Relevant for a coordinate-sorted file containing read pairs only. Maximum number of file handles to keep open when spilling mate info to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the 'ulimit -n' command on a Unix system.

int  8000  [ [ -∞  ∞ ] ]

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--MAX_OUTPUT / -MO

The maximum number of lines output in verbose mode

Integer  100  [ [ -∞  ∞ ] ]

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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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--MODE / -M

Mode of output

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

VERBOSE

SUMMARY

Mode  VERBOSE

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--OUTPUT / -O

Output file or standard out if missing

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.

File  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--SKIP_MATE_VALIDATION / -SMV

If true, this tool will not attempt to validate mate information. In general cases, this option should not be used. However, in cases where samples have very high duplication or chimerism rates (> 10%), the mate validation process often requires extremely large amounts of memory to run, so this flag allows you to forego that check.

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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--VALIDATE_INDEX / NA

DEPRECATED. Use INDEX_VALIDATION_STRINGENCY instead. If true and input is a BAM file with an index file, also validates the index. Until this parameter is retired VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index.

boolean  true

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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 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.