GroupedSVCluster (BETA) – GATK

Clusters structural variants grouping by type, size, and track overlap

Category Structural Variant Discovery

Overview

Clusters structural variants using the same base algorithms as {@link SVCluster}. In addition, variants are grouped according to customizable stratification criteria including:

SV type
Size range
Reference track overlap

The first step is to define these groups in a stratification configuration TSV file. Please see the {@link SVStratify} tool for a description of the stratification method and expected table format.

Each SV is only clustered with other SVs in its own group. Each group must be mutually exclusive, meaning that any given SV should only belong to one group. Furthermore, SVs that do not fall into any of the groups will not be clustered.

The second step is to define the clustering configuration for each group. This is again done by creating a TSV file with the following columns defined on the first line:

NAME
RECIPROCAL_OVERLAP
SIZE_SIMILARITY
BREAKEND_WINDOW
SAMPLE_OVERLAP

where NAME corresponds to the same name given in the stratification configuration. Every group needs to be given a configuration here. That is, there should be a 1:1 correspondence of the rows in the two configuration files (order does not matter).

The remaining columns define the clustering parameters for the group. See {@link SVCluster} for more information on the different parameters. Note that, unlike {@link SVCluster}, distinct parameter sets for depth-only, PESR, and "mixed" clustering cannot be defined for this tool. Instead, the same parameters are applied to all three cases.

For example,

NAME	RECIPROCAL_OVERLAP	SIZE_SIMILARITY	BREAKEND_WINDOW	SAMPLE_OVERLAP
DEL_large_SD	0.3	0.5	1000000	0.1
DUP_large_SD	0.3	0.5	1000000	0.1
DEL_small_SR_RM	0.5	0.5	100	0.1
DUP_small_SR_RM	0.5	0.5	100	0.1
INS_SR	0.5	0.5	100	0

This tool accepts multiple VCF inputs with no restrictions on site or sample overlap.

This tool does not support CNV defragmentation via the {@link #algorithm} parameter.

Inputs

One or more SV VCFs
Stratification configuration TSV file
Clustering configuration TSV file
Reference fasta

Output

Clustered VCF

Usage example

     gatk GroupedSVCluster \
       -R reference.fasta \
       -V variants.vcf.gz \
       -O clustered.vcf.gz \
       --track-name repeatmasker \
       --track-intervals repeatmasker.bed \
       --stratify-config strata.tsv \
       --clustering-config cluster.tsv

@author Mark Walker <markw@broadinstitute.org>

Additional Information

Read filters

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

WellformedReadFilter

GroupedSVCluster 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
--clustering-config		Configuration file (.tsv) containing the clustering parameters for each group
--output -O		Output VCF
--ploidy-table		Sample ploidy table (.tsv)
--reference -R		Reference sequence file
--stratify-config		Stratification configuration file (.tsv)
--variant -V		One or more VCF files containing variants
Optional Tool Arguments
--algorithm	SINGLE_LINKAGE	Clustering algorithm
--alt-allele-summary-strategy	COMMON_SUBTYPE	Strategy to use for choosing a representative alt allele for non-CNV biallelic sites with different subtypes.
--arguments_file		read one or more arguments files and add them to the command line
--breakpoint-summary-strategy	REPRESENTATIVE	Strategy to use for choosing a representative value for a breakpoint cluster.
--cloud-index-prefetch-buffer -CIPB	-1	Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
--cloud-prefetch-buffer -CPB	40	Size of the cloud-only prefetch buffer (in MB; 0 to disable).
--default-no-call	false	Default to no-call GT (e.g. ./.) instead of reference alleles (e.g. 0/0) when a genotype is not available
--disable-bam-index-caching -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.
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--enable-cnv	false	Enable clustering DEL/DUP variants together as CNVs (does not apply to CNV defragmentation)
--fast-mode	false	Fast mode. Drops hom-ref and missing genotype fields and emits them as missing.
--flag-field-logic	OR	Logic for collapsing Flag type INFO and FORMAT fields
--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. User must have storage.buckets.get permission on the bucket being 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
--max-records-in-ram	10000	When writing VCF 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 a VCF file, and increases the amount of RAM needed.
--omit-members	false	Omit cluster member ID annotations
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--stratify-num-breakpoint-overlaps	1	Minimum number of variant endpoint overlaps for tracks
--stratify-num-breakpoint-overlaps-interchromosomal	1	Minimum number of breakpoint overlaps for tracks for interchromosomal variants (e.g. BNDs)
--stratify-overlap-fraction	0.0	Minimum overlap fraction for tracks
--track-intervals		Track intervals file. Can be specified multiple times.
--track-name		Track names. Must be once for each --track-intervals
--variant-prefix		If supplied, generate variant IDs with this prefix
--version	false	display the version number for this tool
Optional Common Arguments
--add-output-sam-program-record	true	If true, adds a PG tag to created SAM/BAM/CRAM files.
--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/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5 -OBM	false	If true, create a MD5 digest for any BAM/SAM/CRAM file created
--create-output-variant-index -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5 -OVM	false	If true, create a a MD5 digest any VCF file created.
--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		A configuration file to use with the GATK.
--input -I		BAM/SAM/CRAM file containing reads
--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
--inverted-read-filter -XRF		Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
--lenient -LE	false	Lenient processing of VCF files
--max-variants-per-shard	0	If non-zero, partitions VCF output into shards, each containing up to the given number of records.
--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.
--seconds-between-progress-updates	10.0	Output traversal statistics every time this many seconds elapse
--sequence-dictionary		Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--tmp-dir		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
--variant-output-filtering		Restrict the output variants to ones that match the specified intervals according to the specified matching mode.

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-output-sam-program-record / -add-output-sam-program-record

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

boolean true

--add-output-vcf-command-line / -add-output-vcf-command-line

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

boolean true

--algorithm

Clustering algorithm

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

DEFRAGMENT_CNV: Defragment cnv cluster algorithm. Not supported with stratification.
SINGLE_LINKAGE: Single linkage cluster algorithm.
MAX_CLIQUE: Max clique cluster algorithm.

CLUSTER_ALGORITHM SINGLE_LINKAGE

--alt-allele-summary-strategy

Strategy to use for choosing a representative alt allele for non-CNV biallelic sites with different subtypes.

The --alt-allele-summary-strategy argument is an enumerated type (AltAlleleSummaryStrategy), which can have one of the following values:

MOST_SPECIFIC_SUBTYPE: Use the most specific subtype that doesn't conflict with any of the other alleles. For example, ( INS , INS:MEI:SVA , INS:MEI:LINE ) results in INS:MEI .
COMMON_SUBTYPE: Use subtypes in common among all alleles. For example, ( INS , INS:MEI:SVA , INS:MEI ) results in INS .

AltAlleleSummaryStrategy COMMON_SUBTYPE

--arguments_file

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

List[File] []

--breakpoint-summary-strategy

Strategy to use for choosing a representative value for a breakpoint cluster.

The --breakpoint-summary-strategy argument is an enumerated type (BreakpointSummaryStrategy), which can have one of the following values:

MEDIAN_START_MEDIAN_END: Use the (first) middle value to summarize cluster starts and ends, such that the start and end were seen in the data
MIN_START_MAX_END: A conservative strategy to summarize a cluster by its smallest extent
MAX_START_MIN_END: A permissive strategy to summarize a cluster by it largest extent
MEAN_START_MEAN_END: Summarize a cluster using the mean value for each end, even if that value was not represented in any sample
REPRESENTATIVE: Picks a single representative call closest to the overall cluster

BreakpointSummaryStrategy REPRESENTATIVE

--cloud-index-prefetch-buffer / -CIPB

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

int -1 [ [ -∞ ∞ ] ]

--cloud-prefetch-buffer / -CPB

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

int 40 [ [ -∞ ∞ ] ]

--clustering-config

Configuration file (.tsv) containing the clustering parameters for each group
Expected format is tab-delimited and contains columns NAME, RECIPROCAL_OVERLAP, SIZE_SIMILARITY, BREAKEND_WINDOW, SAMPLE_OVERLAP. First line must be a header with column names. Comment lines starting with are ignored.

R GATKPath null

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

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

boolean true

--create-output-bam-md5 / -OBM

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

boolean false

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

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

boolean true

--create-output-variant-md5 / -OVM

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

boolean false

--default-no-call

Default to no-call GT (e.g. ./.) instead of reference alleles (e.g. 0/0) when a genotype is not available
Default genotypes are assigned when they cannot be inferred from the inputs, such as when VCFs with different variants and samples are provided.

boolean false

--disable-bam-index-caching / -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

--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

--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

--enable-cnv

Enable clustering DEL/DUP variants together as CNVs (does not apply to CNV defragmentation)
When enabled, DEL and DUP variants will be clustered together. The resulting records with have an SVTYPE of CNV.

boolean false

--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). strings gathered from the command line -XL argument to be parsed into intervals to exclude

List[String] []

--fast-mode

Fast mode. Drops hom-ref and missing genotype fields and emits them as missing.
Results in substantial space and time costs for large sample sets by clearing genotypes that are not needed for clustering, but any associated annotation fields will be set to null in the output.

boolean false

--flag-field-logic

Logic for collapsing Flag type INFO and FORMAT fields

The --flag-field-logic argument is an enumerated type (FlagFieldLogic), which can have one of the following values:

AND: Require all members to have the flag set
OR: Require at least one member to have the flag set
ALWAYS_FALSE: Always set to false

FlagFieldLogic OR

--gatk-config-file

A configuration file to use with the GATK.

String null

--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

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String ""

--help / -h

display the help message

boolean false

--input / -I

BAM/SAM/CRAM file containing reads

List[GATKPath] []

--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

--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] []

--inverted-read-filter / -XRF

Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).

List[String] []

--lenient / -LE

Lenient processing of VCF files

boolean false

--max-records-in-ram

When writing VCF 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 a VCF file, and increases the amount of RAM needed.

int 10000 [ [ -∞ ∞ ] ]

--max-variants-per-shard

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int 0 [ [ 0 ∞ ] ]

--omit-members

Omit cluster member ID annotations

boolean false

--output / -O

Output VCF

R GATKPath null

--ploidy-table

Sample ploidy table (.tsv)
Expected format is tab-delimited and contains a header with the first column SAMPLE and remaining columns contig names. Each row corresponds to a sample, with the sample ID in the first column and contig ploidy integers in their respective columns.

R GATKPath null

--QUIET

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[GATKPath] []

--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

--reference / -R

Reference sequence file

R GATKPath null

--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double 10.0 [ [ -∞ ∞ ] ]

--sequence-dictionary / -sequence-dictionary

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

GATKPath null

--showHidden / -showHidden

display hidden arguments

boolean false

--sites-only-vcf-output

If true, don't emit genotype fields when writing vcf file output.

boolean false

--stratify-config

Stratification configuration file (.tsv)
Expected format is tab-delimited and contains columns NAME, SVTYPE, MIN_SIZE, MAX_SIZE, track. First line must be a header with column names. Comment lines starting with are ignored.

R GATKPath null

--stratify-num-breakpoint-overlaps

Minimum number of variant endpoint overlaps for tracks

int 1 [ [ 0 2 ] ]

--stratify-num-breakpoint-overlaps-interchromosomal

Minimum number of breakpoint overlaps for tracks for interchromosomal variants (e.g. BNDs)

int 1 [ [ 1 2 ] ]

--stratify-overlap-fraction

Minimum overlap fraction for tracks

double 0.0 [ [ 0 1 ] ]

--tmp-dir

Temp directory to use.

GATKPath null

--track-intervals

Track intervals file. Can be specified multiple times.

List[GATKPath] []

--track-name

Track names. Must be once for each --track-intervals

List[String] []

--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

--variant / -V

One or more VCF files containing variants

R List[GATKPath] []

--variant-output-filtering

Restrict the output variants to ones that match the specified intervals according to the specified matching mode.

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

STARTS_IN: starts within any of the given intervals
ENDS_IN: ends within any of the given intervals
OVERLAPS: overlaps any of the given intervals
CONTAINED: contained completely within a contiguous block of intervals without overlap
ANYWHERE: no filtering

Mode null

--variant-prefix

If supplied, generate variant IDs with this prefix

String null

--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 4.6.2.0 built at Sun, 13 Apr 2025 15:34:15 -0400.

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Articles in this section

Category Structural Variant Discovery

Overview

Inputs

Output

Usage example

Additional Information

Read filters

GroupedSVCluster specific arguments

Argument details

--add-output-sam-program-record / -add-output-sam-program-record

--add-output-vcf-command-line / -add-output-vcf-command-line

--cloud-index-prefetch-buffer / -CIPB

--cloud-prefetch-buffer / -CPB

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

--create-output-bam-md5 / -OBM

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

--create-output-variant-md5 / -OVM

--disable-bam-index-caching / -DBIC

--disable-read-filter / -DF

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

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

--exclude-intervals / -XL

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

--help / -h

--input / -I

--interval-exclusion-padding / -ixp

--interval-merging-rule / -imr

--interval-padding / -ip

--interval-set-rule / -isr

--intervals / -L

--inverted-read-filter / -XRF

--lenient / -LE

--output / -O

--read-filter / -RF

--read-index / -read-index

--read-validation-stringency / -VS

--reference / -R

--seconds-between-progress-updates / -seconds-between-progress-updates

--sequence-dictionary / -sequence-dictionary

--showHidden / -showHidden

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

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

--variant / -V

--verbosity / -verbosity