Reverts SAM or BAM files to a previous state.

Category Read Data Manipulation

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Overview

Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.

This tool removes or restores certain properties of the SAM records, including alignment information. It can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score recalibration (BQSR) if the original qualities were retained during the calibration (in the OQ tag).

Usage Examples

Output to a single file

 gatk RevertSamSpark  \\
      -I input.bam \\
      -O reverted.bam
 

Output by read group into multiple files with sample map

 gatk RevertSamSpark \\
      -I input.bam \\
      --output-by-readgroup \\
      --output-map reverted_bam_paths.tsv
 

Output by read group with no output map

 gatk RevertSamSpark \\
      -I input.bam \\
      --output-by-readgroup \\
      -O /write/reverted/read/group/bams/in/this/dir
 

This will output a BAM (Can be overridden with outputByReadgroupFileFormat option.)
Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will be obviated when the keepAlignmentInformation option is used).

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Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by RevertSamSpark.

• AllowAllReadsReadFilter

RevertSamSpark 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	[]	BAM/SAM/CRAM file containing reads
--output  -O	null	The output SAM/BAM file to create, or an output directory if '--output-by-readgroup' is set.
--output-map	null	Tab separated file with two columns, OUTPUT_MAP_READ_GROUP_FIELD_NAME and OUTPUT_MAP_OUTPUT_FILE_FIELD_NAME, providing file mapping only used if '--output-by-readgroup' is set.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--attributes-to-clear	[]	When removing alignment information, the set of optional tags to remove.
--bam-partition-size	0	maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).
--conf	[]	spark properties to set on the spark context in the format =
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--dont-restore-original-qualities	false	Set to prevent the tool from setting the OQ field to the QUAL where available.
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays	""	Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help  -h	false	display the help message
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L	[]	One or more genomic intervals over which to operate
--keep-alignment-information	false	Don't remove any of the alignment information from the file.
--keep-first-duplicate	false	If 'sanitize' only one record when we find more than one record with the same name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the duplicate flag in the FLAG field, but instead reads with the same name.
--library-name	null	The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same library name.
--num-reducers	0	For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.
--output-by-readgroup	false	When true, outputs each read group in a separate file.
--output-by-readgroup-file-format	dynamic	When using --output-by-readgroup, the output file format can be set to a certain format.
--output-shard-tmp-dir	null	when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used
--program-name	null	Name of the program running
--reference  -R	null	Reference sequence
--remove-default-attributes-to-clear	false	When removing alignment information, the set of optional tags to remove.
--remove-duplicate-information	false	By default we remove duplicate read flags from all reads. Note that if this is true, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates.
--sample-alias  -ALIAS	null	The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias.
--sanitize	false	WARNING: This option is potentially destructive. If enabled will discard reads in order to produce a consistent output BAM. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option should only be enabled if the output sort order is queryname and will always cause sorting to occur.
--sharded-output	false	For tools that write an output, write the output in multiple pieces (shards)
--sort-order  -SO	queryname	The sort order to create the reverted output file with, defaults to whatever is specified in the current file
--spark-master	local[*]	URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
--version	false	display the version number for this tool
Optional Common Arguments
--add-output-vcf-command-line	true	If true, adds a command line header line to created VCF files.
--create-output-bam-index  -OBI	true	If true, create a BAM index when writing a coordinate-sorted BAM file.
--create-output-bam-splitting-index	true	If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
--create-output-variant-index  -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--disable-read-filter  -DF	[]	Read filters to be disabled before analysis
--disable-tool-default-read-filters	false	Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
--exclude-intervals  -XL	[]	One or more genomic intervals to exclude from processing
--gatk-config-file	null	A configuration file to use with the GATK.
--interval-exclusion-padding  -ixp	0	Amount of padding (in bp) to add to each interval you are excluding.
--interval-padding  -ip	0	Amount of padding (in bp) to add to each interval you are including.
--interval-set-rule  -isr	UNION	Set merging approach to use for combining interval inputs
--QUIET	false	Whether to suppress job-summary info on System.err.
--read-filter  -RF	[]	Read filters to be applied before analysis
--read-index	[]	Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
--read-validation-stringency  -VS	SILENT	Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--tmp-dir	null	Temp directory to use.
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--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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--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean  true

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--arguments_file / NA

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

List[File]  []

---

--attributes-to-clear / NA

When removing alignment information, the set of optional tags to remove.

Set[String]  []

---

--bam-partition-size / NA

maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).

long  0  [ [ -∞  ∞ ] ]

---

--conf / -conf

spark properties to set on the spark context in the format =

List[String]  []

---

--create-output-bam-index / -OBI

If true, create a BAM index when writing a coordinate-sorted BAM file.

boolean  true

---

--create-output-bam-splitting-index / NA

If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.

boolean  true

---

--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

---

--disable-read-filter / -DF

Read filters to be disabled before analysis

List[String]  []

---

--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation

If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!

boolean  false

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--disable-tool-default-read-filters / -disable-tool-default-read-filters

Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)

boolean  false

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--dont-restore-original-qualities / NA

Set to prevent the tool from setting the OQ field to the QUAL where available.

boolean  false

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--exclude-intervals / -XL

One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals).

List[String]  []

---

--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

---

--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""

---

--help / -h

display the help message

boolean  false

---

--input / -I

BAM/SAM/CRAM file containing reads

R List[String]  []

---

--interval-exclusion-padding / -ixp

Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

---

--interval-merging-rule / -imr

Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:

ALL

OVERLAPPING_ONLY

IntervalMergingRule  ALL

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--interval-padding / -ip

Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

int  0  [ [ -∞  ∞ ] ]

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--interval-set-rule / -isr

Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:

UNION

Take the union of all intervals

INTERSECTION

Take the intersection of intervals (the subset that overlaps all intervals specified)

IntervalSetRule  UNION

---

--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

---

--keep-alignment-information / NA

Don't remove any of the alignment information from the file.

boolean  false

---

--keep-first-duplicate / NA

If 'sanitize' only one record when we find more than one record with the same name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the duplicate flag in the FLAG field, but instead reads with the same name.

boolean  false

---

--library-name / NA

The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same library name.

String  null

---

--num-reducers / NA

For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.

int  0  [ [ -∞  ∞ ] ]

---

--output / -O

The output SAM/BAM file to create, or an output directory if '--output-by-readgroup' is set.

Exclusion: This argument cannot be used at the same time as output-map.

R String  null

---

--output-by-readgroup / NA

When true, outputs each read group in a separate file.

boolean  false

---

--output-by-readgroup-file-format / NA

When using --output-by-readgroup, the output file format can be set to a certain format.

The --output-by-readgroup-file-format argument is an enumerated type (FileType), which can have one of the following values:

sam

bam

cram

dynamic

FileType  dynamic

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--output-map / NA

Tab separated file with two columns, OUTPUT_MAP_READ_GROUP_FIELD_NAME and OUTPUT_MAP_OUTPUT_FILE_FIELD_NAME, providing file mapping only used if '--output-by-readgroup' is set.

Exclusion: This argument cannot be used at the same time as output.

R String  null

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--output-shard-tmp-dir / NA

when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used

Exclusion: This argument cannot be used at the same time as sharded-output.

String  null

---

--program-name / NA

Name of the program running

String  null

---

--QUIET / NA

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

Boolean  false

---

--read-filter / -RF

Read filters to be applied before analysis

List[String]  []

---

--read-index / -read-index

Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.

List[String]  []

---

--read-validation-stringency / -VS

Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value 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 --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT

LENIENT

SILENT

ValidationStringency  SILENT

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--reference / -R

Reference sequence

String  null

---

--remove-default-attributes-to-clear / NA

When removing alignment information, the set of optional tags to remove.

boolean  false

---

--remove-duplicate-information / NA

By default we remove duplicate read flags from all reads. Note that if this is true, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates.

boolean  false

---

--sample-alias / -ALIAS

The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias.

String  null

---

--sanitize / NA

WARNING: This option is potentially destructive. If enabled will discard reads in order to produce a consistent output BAM. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option should only be enabled if the output sort order is queryname and will always cause sorting to occur.

boolean  false

---

--sharded-output / NA

For tools that write an output, write the output in multiple pieces (shards)

Exclusion: This argument cannot be used at the same time as output-shard-tmp-dir.

boolean  false

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--sort-order / -SO

The sort order to create the reverted output file with, defaults to whatever is specified in the current file

The --sort-order argument is an enumerated type (SortOrder), which can have one of the following values:

unsorted

queryname

coordinate

duplicate

unknown

SortOrder  queryname

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--spark-master / NA

URL of the Spark Master to submit jobs to when using the Spark pipeline runner.

String  local[*]

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--tmp-dir / NA

Temp directory to use.

String  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

---

--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

---

--verbosity / -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 / NA

display the version number for this tool

boolean  false

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GATK version 4.1.1.0 built at Sat, 23 Nov 2019 17:58:14 -0500.