SplitReads

Outputs reads from a SAM/BAM/CRAM by read group, sample and library name

Category SAM/BAM/CRAM Tools


Overview


Additional Information

Read filters

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

SplitReads 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
Optional Tool Arguments
--arguments_file
 -
[] read one or more arguments files and add them to the command line
--cloudIndexPrefetchBuffer
 -CIPB
-1 Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloudPrefetchBuffer
 -CPB
40 Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--disableBamIndexCaching
 -DBIC
false If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
--help
 -h
false display the help message
--intervals
 -L
[] One or more genomic intervals over which to operate
--output
 -O
The directory to output SAM/BAM/CRAM files.
--reference
 -R
null Reference sequence
--splitLibraryName
 -LB
false Split file by library.
--splitReadGroup
 -RG
false Split file by read group.
--splitSample
 -SM
false Split file by sample.
--version
 -
false display the version number for this tool
Optional Common Arguments
--addOutputSAMProgramRecord
true If true, adds a PG tag to created SAM/BAM/CRAM files.
--addOutputVCFCommandLine
true If true, adds a command line header line to created VCF files.
--createOutputBamIndex
 -OBI
true If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--createOutputBamMD5
 -OBM
false If true, create a MD5 digest for any BAM/SAM/CRAM file created
--createOutputVariantIndex
 -OVI
true If true, create a VCF index when writing a coordinate-sorted VCF file.
--createOutputVariantMD5
 -OVM
false If true, create a a MD5 digest any VCF file created.
--disableReadFilter
 -DF
[] Read filters to be disabled before analysis
--disableSequenceDictionaryValidation
false If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--disableToolDefaultReadFilters
false Disable all tool default read filters
--excludeIntervals
 -XL
[] One or more genomic intervals to exclude from processing
--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
--lenient
 -LE
false Lenient processing of VCF files
--QUIET
 -
false Whether to suppress job-summary info on System.err.
--readFilter
 -RF
[] Read filters to be applied before analysis
--readIndex
[] 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.
--readValidationStringency
 -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.
--secondsBetweenProgressUpdates
10.0 Output traversal statistics every time this many seconds elapse
--sequenceDictionary
null Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--TMP_DIR
 -
[] Undocumented option
--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.


--addOutputSAMProgramRecord / -addOutputSAMProgramRecord

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true


--addOutputVCFCommandLine / -addOutputVCFCommandLine

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

boolean  true


--arguments_file / -

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

List[File]  []


--cloudIndexPrefetchBuffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]


--cloudPrefetchBuffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]


--createOutputBamIndex / -OBI

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

boolean  true


--createOutputBamMD5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false


--createOutputVariantIndex / -OVI

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

boolean  true


--createOutputVariantMD5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean  false


--disableBamIndexCaching / -DBIC

If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.

boolean  false


--disableReadFilter / -DF

Read filters to be disabled before analysis

List[String]  []


--disableSequenceDictionaryValidation / -disableSequenceDictionaryValidation

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

boolean  false


--disableToolDefaultReadFilters / -disableToolDefaultReadFilters

Disable all tool default read filters

boolean  false


--excludeIntervals / -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]  []


--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_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  [ [ -∞  ∞ ] ]


--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]  []


--lenient / -LE

Lenient processing of VCF files

boolean  false


--output / -O

The directory to output SAM/BAM/CRAM files.

File


--QUIET / -

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

Boolean  false


--readFilter / -RF

Read filters to be applied before analysis

List[String]  []


--readIndex / -readIndex

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]  []


--readValidationStringency / -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 --readValidationStringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  SILENT


--reference / -R

Reference sequence

String  null


--secondsBetweenProgressUpdates / -secondsBetweenProgressUpdates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]


--sequenceDictionary / -sequenceDictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--splitLibraryName / -LB

Split file by library.

boolean  false


--splitReadGroup / -RG

Split file by read group.

boolean  false


--splitSample / -SM

Split file by sample.

boolean  false


--TMP_DIR / -

Undocumented option

List[File]  []


--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 / -

display the version number for this tool

boolean  false


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GATK version 4.beta.2-SNAPSHOT built at 21-33-2017 11:33:43.