Adds gene overlap and variant consequence annotations to SV VCF from GATK-SV pipeline

Category Structural Variant Discovery

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Overview

Adds gene overlap, predicted functional consequence, and noncoding element overlap annotations to a structural variant (SV) VCF from the GATK-SV pipeline.

Inputs

• VCF containing structural variant (SV) records from the GATK-SV pipeline
• GTF file containing primary or canonical transcripts (optional; required for protein-coding gene, transcription start site, and promoter overlap annotations)
• BED file of noncoding elements in which the fourth column specifies the type of element (optional; required for noncoding element overlap annotations)

Output

• Annotated VCF

Usage example

     gatk SVAnnotate \
       -V structural.vcf.gz \
       --protein-coding-gtf canonical.gtf \
       --non-coding-bed noncoding.bed \
       -O annotated.vcf.gz
 

Annotation categories

If a variant overlaps a gene, promoter, or noncoding element, the predicted functional impact will be annotated and the gene or noncoding element name listed. The list below describes the functional consequence categories in more detail. For complex variants (CPX), the annotations represent the union of the independent annotations of each component of the complex event according to its coordinates and SV type.

• PREDICTED_LOF
  Gene(s) on which the SV is predicted to have a loss-of-function (LOF) effect. The conditions for a LOF consequence depend on the SV type:

  • Deletion (DEL): the deletion overlaps any coding sequence (CDS) or the TSS
  • Duplication (DUP): the duplication has both breakpoints in CDS, or one breakpoint in CDS and another in the 3' or 5' untranslated region (UTR)
  • Insertion (INS): the insertion falls within CDS
  • Inversion (INV): the inversion overlaps any coding sequence (CDS) or the TSS, except if it spans the entire gene (PREDICTED_INV_SPAN)
  • Translocation (CTX): any translocation breakpoint falls within the transcript
  • Multiallelic copy number variant (CNV): not annotated as PREDICTED_LOF. See PREDICTED_MSV_EXON_OVERLAP
  • Breakend (BND): not annotated as PREDICTED_LOF. See PREDICTED_BREAKEND_EXONIC

• PREDICTED_COPY_GAIN
  Gene(s) on which the SV is predicted to have a copy-gain effect. This occurs when a duplication spans the entire transcript, from the first base of the 5' UTR to the last base of the 3' UTR.

• PREDICTED_INTRAGENIC_EXON_DUP
  Gene(s) on which the SV is predicted to result in intragenic exonic duplication without breaking any coding sequences. This occurs when a duplication spans at least one coding exon and neither breakpoint is in CDS; both breakpoints are in UTR or intron. The result is that intact exons are duplicated within the boundaries of the gene body.

• PREDICTED_PARTIAL_EXON_DUP
  Gene(s) where the duplication SV has one breakpoint in the coding sequence. This occurs when a duplication has exactly one breakpoint in CDS and the other breakpoint is in intron or UTR. When the duplication is in tandem, the result is that the endogenous copy of the breakpoint-harboring exon remains intact and a partial duplicate copy of that exon is also found elsewhere in the same gene.

• PREDICTED_TSS_DUP
  Gene(s) for which the SV is predicted to duplicate the transcription start site (TSS). This occurs when a duplication has one breakpoint before the start of a transcript and the other breakpoint within the transcript. When the duplication is in tandem, the result is that there is one intact copy of the full endogenous gene, but an additional transcription start site is duplicated upstream (5') of the endogenous TSS.

• PREDICTED_DUP_PARTIAL
  Gene(s) which are partially overlapped by an SV's duplication, but the transcription start site is not duplicated. The partial duplication occurs when a duplication has one breakpoint within the transcript and one breakpoint after the end of the transcript. When the duplication is in tandem, the result is that there is one intact copy of the full endogenous gene.

• PREDICTED_INV_SPAN
  Gene(s) which are entirely spanned by an SV's inversion. A whole-gene inversion occurs when an inversion spans the entire transcript, from the first base of the 5' UTR to the last base of the 3' UTR.

• PREDICTED_MSV_EXON_OVERLAP
  Gene(s) on which the multiallelic CNV would be predicted to have a LOF, INTRAGENIC_EXON_DUP, COPY_GAIN, DUP_PARTIAL, TSS_DUP, or PARTIAL_EXON_DUP annotation if the SV were biallelic. The functional impact of the multiallelic CNV on an individual sample depends on the copy number of the individual.

• PREDICTED_UTR
  Gene(s) for which the SV is predicted to disrupt a UTR. This occurs when the SV has at least one breakpoint in a gene's 5' or 3' UTR but does not meet any of the criteria for a different gene-disrupting categorization above.

• PREDICTED_INTRONIC
  Gene(s) where the SV was found to lie entirely within an intron.

• PREDICTED_BREAKEND_EXONIC
  Gene(s) for which the SV breakend is predicted to fall in an exon. This category is reserved for breakend (BND) SVs with a breakpoint in CDS.

• PREDICTED_INTERGENIC
  SV does not overlap any protein-coding gene transcripts in the GTF.

• PREDICTED_PROMOTER
  Gene(s) for which the SV is predicted to overlap the promoter region. This occurs when the variant overlaps the predicted promoter region but does not overlap the transcript. The promoter region is inferred from the GTF as a window upstream of the TSS. The size of the window can be altered with the --promoter-window-length argument.

• PREDICTED_NEAREST_TSS
  Nearest transcription start site to an intergenic variant. The gene with the nearest TSS to either side of the SV is annotated for intergenic variants that do not overlap any promoter regions.

• PREDICTED_NONCODING_SPAN
  Class(es) of noncoding elements spanned by SV.

• PREDICTED_NONCODING_BREAKPOINT
  Class(es) of noncoding elements disrupted by SV breakpoint.

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Additional Information

Read filters

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

• WellformedReadFilter

SVAnnotate 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
--variant  -V		A VCF file containing 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).
--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-breakend-as-cnv-length	-1	Length in bp. Provide to annotate BNDs smaller than this size as deletions or duplications if applicable. Recommended value: < 2000000
--non-coding-bed		BED file (with header) containing non-coding features. Columns: chrom, start, end, name, score (.), strand
--output  -O		Output file (if not provided, defaults to STDOUT)
--promoter-window-length	1000	Promoter window (bp) upstream of TSS. Promoters will be inferred as the {window} bases upstream of the TSS. Default: 1000
--protein-coding-gtf		Protein-coding GTF file containing primary or canonical transcripts (1-2 transcripts per gene only)
--reference  -R		Reference sequence
--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
--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

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--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  [ [ -∞  ∞ ] ]

---

--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

---

--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).

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-breakend-as-cnv-length

Length in bp. Provide to annotate BNDs smaller than this size as deletions or duplications if applicable. Recommended value: < 2000000

int  -1  [ [ 0  ∞ ] ]

---

--max-variants-per-shard

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

int  0  [ [ 0  ∞ ] ]

---

--non-coding-bed

BED file (with header) containing non-coding features. Columns: chrom, start, end, name, score (.), strand

File  null

---

--output / -O

Output file (if not provided, defaults to STDOUT)

GATKPath  null

---

--promoter-window-length

Promoter window (bp) upstream of TSS. Promoters will be inferred as the {window} bases upstream of the TSS. Default: 1000

int  1000  [ [ 0  ∞ ] ]

---

--protein-coding-gtf

Protein-coding GTF file containing primary or canonical transcripts (1-2 transcripts per gene only)

File  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

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

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--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

A VCF file containing variants

R GATKPath  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 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.