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**BETA** JointGermlineCNVSegmentation

Combine segmented gCNV VCFs.

Category Structural Variant Discovery

Overview

Merge GCNV segments VCFs This tool takes in segmented VCFs produced by {@link PostprocessGermlineCNVCalls}. For single-sample input VCFs, the tool defragments CNV calls by merging adjacent events within the default or specified fractional padding margins. For distinct samples, the tool clusters events that meet the reciprocal overlap requirement. Output is a multi-sample VCF with site allele counts and frequencies (AC, AF). This tool can also be run on multiple multi-sample VCFs, as in a hierarchical gather for large cohorts. In this case, defragmentation is not preformed because it is assumed that single-sample defragmentation occurred during the initial tool invocation that produced the multi-sample VCF.

Required inputs

Output

A single multi-sample VCF with genotypes and copy numbers

Usage example

   gatk JointGermlineCNVSegmentation \
         -R reference.fasta
         -V sample1.vcf.gz
         -V sample2.vcf.gz
         --model-call-intervals .filtered.interval_list
         --pedigree XandYassignments.ped
         -O clustered.vcf.gz

Caveats

Additional Information

Read filters

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

JointGermlineCNVSegmentation 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
--output
 -O 		The combined output VCF
--pedigree
 -ped 		Pedigree file for samples
--reference
 -R 		Reference sequence file
--variant
 -V 		One or more VCF files containing variants
Optional Tool Arguments
--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
--autosomal-ref-copy-number
 2 Reference copy-number on autosomal intervals.
--breakpoint-summary-strategy
 MEDIAN_START_MEDIAN_END 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).
--clustering-breakend-window
 10000000 Cluster events whose endpoints are within this distance of each other
--clustering-interval-overlap
 0.8 Minimum interval reciprocal overlap for clustering
--clustering-size-similarity
 0.0 Minimum size similarity for clustering
--defragmentation-padding-fraction
 0.25 Extend events by this fraction on each side when determining overlap to merge
--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!
--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.
--min-sample-set-fraction-overlap
 0.0 Minimum fraction of common samples for two variants to cluster together
--minimum-qs-score
 20 Minimum QS score to combine a variant segment
--model-call-intervals
 gCNV model intervals created with the FilterIntervals tool.
--sites-only-vcf-output
 false If true, don't emit genotype fields when writing vcf file output.
--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
--combine-variants-distance
 0 Maximum distance for variants to be grouped together
--ignore-variants-starting-outside-interval
 false Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)
--max-distance
 2147483647 Maximum distance for variants to be grouped together
--ref-padding
 1 Number of bases on either side to expand spanning reference window
--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

--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]  []

--autosomal-ref-copy-number

Reference copy-number on autosomal intervals.

int  2  [ [ 0  ∞ ] ]

--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  MEDIAN_START_MEDIAN_END

--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-breakend-window

Cluster events whose endpoints are within this distance of each other

int  10000000  [ [ -∞  ∞ ] ]

--clustering-interval-overlap

Minimum interval reciprocal overlap for clustering

double  0.8  [ [ -∞  ∞ ] ]

--clustering-size-similarity

Minimum size similarity for clustering

double  0.0  [ [ -∞  ∞ ] ]

--combine-variants-distance

Maximum distance for variants to be grouped together

int  0  [ [ -∞  ∞ ] ]

--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

--defragmentation-padding-fraction

Extend events by this fraction on each side when determining overlap to merge

double  0.25  [ [ -∞  ∞ ] ]

--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

--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]  []

--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

--ignore-variants-starting-outside-interval

Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)
this option has no effect unless intervals are specified. This exists to mimic GATK3 interval traversal patterns

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-distance

Maximum distance for variants to be grouped together

int  2147483647  [ [ -∞  ∞ ] ]

--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  ∞ ] ]

--min-sample-set-fraction-overlap

Minimum fraction of common samples for two variants to cluster together

double  0.0  [ [ -∞  ∞ ] ]

--minimum-qs-score

Minimum QS score to combine a variant segment

int  20  [ [ -∞  ∞ ] ]

--model-call-intervals

gCNV model intervals created with the FilterIntervals tool.

GATKPath  null

--output / -O

The combined output VCF

R GATKPath  null

--pedigree / -ped

Pedigree file for samples
See https://software.broadinstitute.org/gatk/documentation/article.php?id=7696 for more details on the PED format. Note that each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to tell the GATK PED parser that the corresponding fields are missing from the ped file.

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

--ref-padding

Number of bases on either side to expand spanning reference window

int  1  [ [ -∞  ∞ ] ]

--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

--tmp-dir

Temp directory to use.

GATKPath  null

--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

--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 13:21:43 -0400.