Clusters structural variants
Clusters structural variants based on coordinates, event type, and supporting algorithms. Primary use cases include:
Clustering tasks can be accomplished using one of two algorithms. The SINGLE_LINKAGE algorithm produces clusters for which all members cluster with at least one other member. The MAX_CLIQUE algorithm, however, requires that all members cluster with every other member. The latter is in general non-polynomial in time and space but implemented to minimize computations by traversing variants ordered by start position and efficiently finalizing "active" clusters that are determined to be complete.
The tool determines whether two given variants should cluster based following criteria:
For CNV defragmentation (DEFRAGMENT_CNV algorithm), the tool uses single-linkage clustering based on the following linkage criteria:
Interval overlap, breakend window, and sample overlap parameters are defined for three combinations of event types using the ALGORITHMS field, which describes the type of evidence that was used to call the variant:
Users must supply one or more VCFs containing SVs with the following info fields:
In addition, the following FORMAT fields must be defined:
Note that for CNVs (DEL, DUP, multi-allelic CNV), GT alleles are set according to the CN/ECN fields. In some cases, (e.g. diploid DUPs with CN 4), allele phasing cannot be determined unambiguously and GT is set with no-call alleles.
The tool generates a new VCF with clusters collapsed into single representative records. By default, a MEMBERS field is generated that lists the input variant IDs contained in that record's cluster.
gatk SVCluster \
-V variants.vcf.gz \
-O clustered.vcf.gz \
--algorithm SINGLE_LINKAGE
@author Mark Walker <markw@broadinstitute.org>
This Read Filter is automatically applied to the data by the Engine before processing by SVCluster.
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 | |||
| --output -O |
Output VCF | ||
| --ploidy-table |
Sample ploidy table (.tsv) | ||
| --reference -R |
Reference sequence file | ||
| --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 | |
| --defrag-padding-fraction |
0.25 | Padding as a fraction of variant length for CNV defragmentation mode. | |
| --defrag-sample-overlap |
0.8 | Minimum sample overlap fraction. Use instead of --depth-sample-overlap in CNV defragmentation mode. | |
| --depth-breakend-window |
10000000 | Depth/Depth window size for breakend proximity | |
| --depth-interval-overlap |
0.8 | Depth/Depth interval reciprocal overlap fraction | |
| --depth-sample-overlap |
0.0 | Depth/Depth shared sample overlap fraction | |
| --depth-size-similarity |
0.0 | Depth/Depth size similarity | |
| --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. | |
| --mixed-breakend-window |
1000 | Depth/PESR window size for breakend proximity | |
| --mixed-interval-overlap |
0.8 | PESR/Depth interval reciprocal overlap fraction | |
| --mixed-sample-overlap |
0.0 | Depth/PESR shared sample overlap fraction | |
| --mixed-size-similarity |
0.0 | Depth/PESR size similarity | |
| --omit-members |
false | Omit cluster member ID annotations | |
| --pesr-breakend-window |
500 | PESR/PESR window size for breakend proximity | |
| --pesr-interval-overlap |
0.5 | PESR/PESR interval reciprocal overlap fraction | |
| --pesr-sample-overlap |
0.0 | PESR/PESR shared sample overlap fraction | |
| --pesr-size-similarity |
0.0 | PESR/PESR size similarity | |
| --sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
| --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. | ||
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
Clustering algorithm
The --algorithm argument is an enumerated type (CLUSTER_ALGORITHM), which can have one of the following values:
CLUSTER_ALGORITHM SINGLE_LINKAGE
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:
AltAlleleSummaryStrategy COMMON_SUBTYPE
read one or more arguments files and add them to the command line
List[File] []
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:
BreakpointSummaryStrategy REPRESENTATIVE
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
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
Padding as a fraction of variant length for CNV defragmentation mode.
double 0.25 [ [ -∞ ∞ ] ]
Minimum sample overlap fraction. Use instead of --depth-sample-overlap in CNV defragmentation mode.
double 0.8 [ [ -∞ ∞ ] ]
Depth/Depth window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster depth-only/depth-only variant pairs.
int 10000000 [ [ 0 ∞ ] ]
Depth/Depth interval reciprocal overlap fraction
Minimum interval reciprocal overlap fraction to cluster depth-only/depth-only variant pairs.
double 0.8 [ [ 0 1 ] ]
Depth/Depth shared sample overlap fraction
Minimum carrier sample reciprocal overlap fraction to cluster depth-only/depth-only variant pairs.
double 0.0 [ [ 0 1 ] ]
Depth/Depth size similarity
Minimum size similarity to cluster depth-only/depth-only variant pairs.
double 0.0 [ [ 0 1 ] ]
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
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
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
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. 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
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:
FlagFieldLogic OR
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
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 ""
display the help message
boolean false
BAM/SAM/CRAM file containing reads
List[GATKPath] []
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 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:
IntervalMergingRule ALL
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 [ [ -∞ ∞ ] ]
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:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
Lenient processing of VCF files
boolean false
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 [ [ -∞ ∞ ] ]
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
Depth/PESR window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster depth-only/PESR variant pairs.
int 1000 [ [ 0 ∞ ] ]
PESR/Depth interval reciprocal overlap fraction
Minimum interval reciprocal overlap fraction to cluster depth-only/PESR variant pairs.
double 0.8 [ [ 0 1 ] ]
Depth/PESR shared sample overlap fraction
Minimum carrier sample reciprocal overlap fraction to cluster depth-only/PESR variant pairs.
double 0.0 [ [ 0 1 ] ]
Depth/PESR size similarity
Minimum size similarity to cluster depth-only/PESR variant pairs.
double 0.0 [ [ 0 1 ] ]
Omit cluster member ID annotations
boolean false
Output VCF
R GATKPath null
PESR/PESR window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster PESR/PESR variant pairs.
int 500 [ [ 0 ∞ ] ]
PESR/PESR interval reciprocal overlap fraction
Minimum interval reciprocal overlap fraction to cluster PESR/PESR variant pairs.
double 0.5 [ [ 0 1 ] ]
PESR/PESR shared sample overlap fraction
Minimum carrier sample reciprocal overlap fraction to cluster PESR/PESR variant pairs.
double 0.0 [ [ 0 1 ] ]
PESR/PESR size similarity
Minimum size similarity to cluster PESR/PESR variant pairs.
double 0.0 [ [ 0 1 ] ]
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
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
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] []
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:
ValidationStringency SILENT
Reference sequence file
R GATKPath null
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Temp directory to use.
GATKPath null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
One or more VCF files containing variants
R List[GATKPath] []
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:
Mode null
If supplied, generate variant IDs with this prefix
String null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.