Tool for adding annotations to VCF files

Category Variant Manipulation

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Overview

Annotate variant calls with context information

This tool is designed to annotate variant calls based on their context (as opposed to functional annotation). Various annotation modules are available; see the "Annotation Modules" page linked in the Tool Documentation sidebar for a complete list.

Input

A variant set to annotate and optionally one or more BAM files.

Output

An annotated VCF.

Usage examples

Annotate a VCF with dbSNP IDs and depth of coverage for each sample

   VariantAnnotator \
   -R reference.fasta \
   -I input.bam \
   -V input.vcf \
   -o output.vcf \
   -A Coverage \
   --dbsnp dbsnp.vcf
 

Annotate a VCF with allele frequency by an external resource. Annotation will only occur if there is allele concordance between the resource and the input VCF

   VariantAnnotator \
   -R reference.fasta \
   -I input.bam \
   -V input.vcf \
   -o output.vcf \
   -L anotherInput.vcf \
   --resource:foo resource.vcf \
   -E foo.AF \
   --resource-allele-concordance
 

Annotate with AF and FILTER fields from an external resource

   VariantAnnotator \
   -R reference.fasta \
   -V input.vcf \
   -o output.vcf \
   --resource:foo resource.vcf \
   --expression foo.AF \
   --expression foo.FILTER
 

Caveat

This tool outputs no annotations by default, all annotations/groups must be specified explicitly.

Special note on RankSumTestAnnotations

RankSumAnnotations produced by this tool are not the same as those produced by the HaplotypeCaller. Without the likelihoods, the tool resorts to a pileup heuristic to categorize reads which means that RankSumAnnotations will only be present for SNP variants.

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Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by VariantAnnotator.

• PassesVendorQualityCheckReadFilter
• MappedReadFilter
• NotDuplicateReadFilter
• PrimaryLineReadFilter
• WellformedReadFilter

VariantAnnotator 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 file to which variants should be written
--variant  -V		A VCF file containing variants
Optional Tool Arguments
--annotation  -A		One or more specific annotations to add to variant calls
--annotation-group  -G		One or more groups of annotations to apply to variant calls
--annotations-to-exclude  -AX		One or more specific annotations to exclude from variant calls
--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).
--dbsnp  -D		dbSNP file
--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!
--expression  -E		One or more specific expressions to apply to variant calls
--flow-order-for-annotations		flow order used for this annotations. [readGroup:]flowOrder
--founder-id		Samples representing the population "founders"
--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
--min-base-quality-score	10	Minimum base quality required to confidently assign a read to an allele
--pedigree  -ped		Pedigree file for determining the population "founders"
--reference  -R		Reference sequence
--resource		External resource VCF file
--resource-allele-concordance  -rac	false	Check for allele concordances when using an external resource VCF file
--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
--comparison  -comp		Comparison VCF file(s)
--disable-tool-default-annotations	false	Disable all tool default annotations
--enable-all-annotations	false	Use all possible annotations (not for the faint of heart)
--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.

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

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

boolean  true

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--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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--annotation / -A

One or more specific annotations to add to variant calls
Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.

List[String]  []

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--annotation-group / -G

One or more groups of annotations to apply to variant calls
Which groups of annotations to add to the output variant calls. Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.

List[String]  []

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--annotations-to-exclude / -AX

One or more specific annotations to exclude from variant calls
Which annotations to exclude from output in the variant calls. Note that this argument has higher priority than the -A or -G arguments, so these annotations will be excluded even if they are explicitly included with the other options.

List[String]  []

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--arguments_file

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

List[File]  []

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

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

int  -1  [ [ -∞  ∞ ] ]

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--cloud-prefetch-buffer / -CPB

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

int  40  [ [ -∞  ∞ ] ]

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--comparison / -comp

Comparison VCF file(s)
If a call overlaps with a record from the provided comp track, the INFO field will be annotated as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comp track will be ignored. Note that 'dbSNP' has been special-cased (see the --dbsnp argument).

List[FeatureInput[VariantContext]]  []

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

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

boolean  true

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

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

boolean  false

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

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

boolean  true

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

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

boolean  false

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--dbsnp / -D

dbSNP file
The rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. Note that dbSNP is not used in any way for the calculations themselves.

FeatureInput[VariantContext]  null

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--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

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--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

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--disable-tool-default-annotations / -disable-tool-default-annotations

Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool

boolean  false

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--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

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--enable-all-annotations

Use all possible annotations (not for the faint of heart)
You can use the -AX argument in combination with this one to exclude specific annotations. Note that some annotations may not be actually applied if they are not applicable to the data provided or if they are unavailable to the tool (e.g. there are several annotations that are currently not hooked up to HaplotypeCaller). At present no error or warning message will be provided, the annotation will simply be skipped silently. You can check the output VCF header to see which annotations were activated and thus might be applied (although this does not guarantee that the annotation was applied to all records in the VCF, since some annotations have additional requirements, e.g. minimum number of samples or heterozygous sites only -- see the documentation for individual annotations' requirements).

boolean  false

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--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]  []

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--expression / -E

One or more specific expressions to apply to variant calls
This option enables you to add annotations from one VCF to another. For example, if you want to annotate your callset with the AC field value from a VCF file named 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' (see the -resource argument, also documented on this page) and you specify '-E my_resource.AC'. In the resulting output VCF, any records for which there is a record at the same position in the resource file will be annotated with 'my_resource.AC=N'. INFO field data, ID, ALT, and FILTER fields may be used as expression values. Note that if there are multiple records in the resource file that overlap the given position, one is chosen randomly.

Set[String]  []

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--flow-order-for-annotations

flow order used for this annotations. [readGroup:]flowOrder

List[String]  []

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--founder-id / -founder-id

Samples representing the population "founders"

List[String]  []

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--gatk-config-file

A configuration file to use with the GATK.

String  null

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--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  [ [ -∞  ∞ ] ]

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--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  ""

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--help / -h

display the help message

boolean  false

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--input / -I

BAM/SAM/CRAM file containing reads

List[GATKPath]  []

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--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  [ [ -∞  ∞ ] ]

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--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

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--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  [ [ -∞  ∞ ] ]

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--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

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--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

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--lenient / -LE

Lenient processing of VCF files

boolean  false

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--max-variants-per-shard

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

int  0  [ [ 0  ∞ ] ]

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--min-base-quality-score

Minimum base quality required to confidently assign a read to an allele
Bases with a quality below this threshold will not be used for annotation.

byte  10  [ [ -∞  ∞ ] ]

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--output / -O

The file to which variants should be written

R File  null

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--pedigree / -ped

Pedigree file for determining the population "founders"

GATKPath  null

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--QUIET

Whether to suppress job-summary info on System.err.

Boolean  false

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--read-filter / -RF

Read filters to be applied before analysis

List[String]  []

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--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]  []

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--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

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--reference / -R

Reference sequence

GATKPath  null

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--resource

External resource VCF file
An external resource VCF file or files from which to annotate. Use this option to add annotations from a resource file to the output. For example, if you want to annotate your callset with the AC field value from a VCF file named 'resource_file.vcf', you tag it with '-resource:my_resource resource_file.vcf' and you additionally specify '-E my_resource.AC' (-E is short for --expression, also documented on this page). In the resulting output VCF, any records for which there is a record at the same position in the resource file will be annotated with 'my_resource.AC=N'. Note that if there are multiple records in the resource file that overlap the given position, one is chosen randomly. Check for allele concordance if using --resource-allele-concordance, otherwise the match is based on position only.

List[FeatureInput[VariantContext]]  []

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--resource-allele-concordance / -rac

Check for allele concordances when using an external resource VCF file
If this argument is specified, add annotations (specified by --expression) from an external resource (specified by --resource) to the input VCF (specified by --variant) only if the alleles are concordant between input and the resource VCFs. Otherwise, always add the annotations.

Boolean  false

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

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

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--sequence-dictionary / -sequence-dictionary

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

GATKPath  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--sites-only-vcf-output

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

boolean  false

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--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

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

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--variant / -V

A VCF file containing variants

R GATKPath  null

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--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

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--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.