Tool for adding annotations to VCF files
Category Variant Manipulation
OverviewAnnotate 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.
A variant set to annotate and optionally one or more BAM files.
An annotated VCF.
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
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.
These Read Filters are automatically applied to the data by the Engine before processing by VariantAnnotator.
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|
|null||The file to whcih variants should be written|
|null||A VCF file containing variants|
|Optional Tool Arguments|
|||One or more specific annotations to add to variant calls|
|||One or more groups of annotations to apply to variant calls|
|||One or more specific annotations to exclude from variant calls|
||||read one or more arguments files and add them to the command line|
|-1||Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.|
|40||Size of the cloud-only prefetch buffer (in MB; 0 to disable).|
|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.|
||false||If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!|
|||One or more specific expressions to apply to variant calls|
||||Samples representing the population "founders"|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
||""||Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.|
|false||display the help message|
|ALL||Interval merging rule for abutting intervals|
|||One or more genomic intervals over which to operate|
||10||Minimum base quality required to confidently assign a read to an allele|
|null||Pedigree file for determining the population "founders"|
||||External resource VCF file|
|false||Check for allele concordances when using an external resource VCF file|
||false||If true, don't emit genotype fields when writing vcf file output.|
||false||display the version number for this tool|
|Optional Common Arguments|
||true||If true, adds a PG tag to created SAM/BAM/CRAM files.|
||true||If true, adds a command line header line to created VCF files.|
|true||If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.|
|false||If true, create a MD5 digest for any BAM/SAM/CRAM file created|
|true||If true, create a VCF index when writing a coordinate-sorted VCF file.|
|false||If true, create a a MD5 digest any VCF file created.|
|||Read filters to be disabled before analysis|
||false||Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)|
|||One or more genomic intervals to exclude from processing|
||null||A configuration file to use with the GATK.|
|||BAM/SAM/CRAM file containing reads|
|0||Amount of padding (in bp) to add to each interval you are excluding.|
|0||Amount of padding (in bp) to add to each interval you are including.|
|UNION||Set merging approach to use for combining interval inputs|
|false||Lenient processing of VCF files|
||false||Whether to suppress job-summary info on System.err.|
|||Read filters to be applied before analysis|
||||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.|
|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.|
||10.0||Output traversal statistics every time this many seconds elapse|
||null||Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.|
||null||Temp directory to use.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
|||Comparison VCF file(s)|
||false||Disable all tool default annotations|
||false||Use all possible annotations (not for the faint of heart)|
||false||display hidden arguments|
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.
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
--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.
--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.
--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.
--arguments_file / NA
read one or more arguments files and add them to the command line
--cloud-index-prefetch-buffer / -CIPB
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--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).
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
If true, create a VCF index when writing a coordinate-sorted VCF file.
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
--dbsnp / -D
A dbSNP VCF file.
--disable-bam-index-caching / -DBIC
--disable-read-filter / -DF
Read filters to be disabled before analysis
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
--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
--disable-tool-default-read-filters / -disable-tool-default-read-filters
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).
--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).
--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.
--founder-id / -founder-id
Samples representing the population "founders"
--gatk-config-file / NA
A configuration file to use with the GATK.
--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 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help / -h
display the help message
--input / -I
BAM/SAM/CRAM file containing reads
--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:
--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:
- Take the union of all intervals
- Take the intersection of intervals (the subset that overlaps all intervals specified)
--intervals / -L
One or more genomic intervals over which to operate
--lenient / -LE
Lenient processing of VCF files
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 [ [ -∞ ∞ ] ]
--output / -O
The file to whcih variants should be written
R File null
--pedigree / -ped
Pedigree file for determining the population "founders"
--QUIET / NA
Whether to suppress job-summary info on System.err.
--read-filter / -RF
Read filters to be applied before analysis
--read-index / -read-index
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
--reference / -R
--resource / NA
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.
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.
--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.
--showHidden / -showHidden
display hidden arguments
If true, don't emit genotype fields when writing vcf file output.
--tmp-dir / NA
Temp directory to use.
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
--variant / -V
A VCF file containing variants
R String null
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
--version / NA
display the version number for this tool
GATK version 18.104.22.168-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.