Annotates structural variant genotype concordance

Category Structural Variant Discovery

---

Overview

This tool calculates SV genotype concordance between an "evaluation" VCF and a "truth" VCF. For each evaluation variant, a single truth variant is matched based on the following order of criteria:

1. Total breakend distance
2. Min breakend distance (among the two sides)
3. Genotype concordance

after meeting minimum overlap criteria. Evaluation variants that are sucessfully matched are annotated with genotype concordance metrics, including allele frequency of the truth variant. See output header for descriptions of the specific fields. Note that genotypes of samples that are present in the evaluation VCF but not the truth VCF are assumed to be no-calls for concordance. For multi-allelic CNVs, only a copy state concordance metric is annotated.

Inputs

• Evaluation VCF
• Truth VCF (equal set or subset of samples)

Output

• The evaluation VCF annotated with genotype concordance metrics

Usage example

     gatk SVConcordance \
       --sequence-dictionary ref.dict \
       --eval evaluation.vcf.gz \
       --truth truth.vcf.gz \
       -O output.vcf.gz
 

@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 SVConcordance.

• WellformedReadFilter

SVConcordance 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
--evaluation  -eval		A VCF containing variants to be compared to the truth
--output  -O		Output VCF
--truth		A VCF containing truth variants
Optional Tool Arguments
--arguments_file		read one or more arguments files and add them to the command line
--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).
--confidence  -C		TO BE IMPLEMENTED
--depth-breakend-window	0	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
--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
--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
--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
--reference  -R		Reference sequence
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--use-truth-af	false	Use allele frequency annotations from the truth vcf from the best-matching record.
--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
--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

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

---

--arguments_file

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

List[File]  []

---

--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  [ [ -∞  ∞ ] ]

---

--confidence / -C

TO BE IMPLEMENTED

File  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

---

--depth-breakend-window

Depth/Depth window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster depth-only/depth-only variant pairs.

int  0  [ [ 0  ∞ ] ]

---

--depth-interval-overlap

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-sample-overlap

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 ] ]

---

--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

---

--evaluation / -eval

A VCF containing variants to be compared to the truth

R String  null

---

--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

---

--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]  []

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

---

--max-variants-per-shard

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

int  0  [ [ 0  ∞ ] ]

---

--mixed-breakend-window

Depth/PESR window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster depth-only/PESR variant pairs.

int  1000  [ [ 0  ∞ ] ]

---

--mixed-interval-overlap

PESR/Depth interval reciprocal overlap fraction
Minimum interval reciprocal overlap fraction to cluster depth-only/PESR variant pairs.

double  0.8  [ [ 0  1 ] ]

---

--mixed-sample-overlap

Depth/PESR shared sample overlap fraction
Minimum carrier sample reciprocal overlap fraction to cluster depth-only/PESR variant pairs.

double  0.0  [ [ 0  1 ] ]

---

--output / -O

Output VCF

R GATKPath  null

---

--pesr-breakend-window

PESR/PESR window size for breakend proximity
Maximum allowed distance between endpoints (in bp) to cluster PESR/PESR variant pairs.

int  500  [ [ 0  ∞ ] ]

---

--pesr-interval-overlap

PESR/PESR interval reciprocal overlap fraction
Minimum interval reciprocal overlap fraction to cluster PESR/PESR variant pairs.

double  0.5  [ [ 0  1 ] ]

---

--pesr-sample-overlap

PESR/PESR shared sample overlap fraction
Minimum carrier sample reciprocal overlap fraction to cluster PESR/PESR variant pairs.

double  0.0  [ [ 0  1 ] ]

---

--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

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

---

--truth / -truth

A VCF containing truth variants

R String  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

---

--use-truth-af

Use allele frequency annotations from the truth vcf from the best-matching record.
By default, truth allele frequencies are calculated on the fly using the evaluation record's allele number as the denominator. This option forces the tool to use the allele frequency annotations (AF/AN/AC) of the closest- matching truth variant record (by min distance to both breakpoints) for truth allele frequency annotations.

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 4.4.0.0 built at Thu, 16 Mar 2023 15:00:37 -0400.