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.
A variant set to annotate and optionally one or more BAM files.
An annotated VCF.
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T VariantAnnotator \ -I input.bam \ -V input.vcf \ -o output.vcf \ -A Coverage \ -L input.vcf \ --dbsnp dbsnp.vcf
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T VariantAnnotator \ -I input.bam \ -V input.vcf \ -o output.vcf \ -L input.vcf \ --resource:foo resource.vcf \ -E foo.AF \ --resourceAlleleConcordance
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T VariantAnnotator \ -V input.vcf \ -o output.vcf \ --resource:foo resource.vcf \ --expression foo.AF \ --expression foo.FILTER
These Read Filters are automatically applied to the data by the Engine before processing by VariantAnnotator.
This tool can be run in multi-threaded mode using this option.
This tool uses a sliding window on the reference.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
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 Inputs | |||
| --variant -V |
NA | Input VCF file | |
| Optional Inputs | |||
| --comp |
[] | Comparison VCF file | |
| --dbsnp -D |
none | dbSNP file | |
| --resource |
[] | External resource VCF file | |
| --snpEffFile |
none | SnpEff file from which to get annotations | |
| Optional Outputs | |||
| --out -o |
stdout | File to which variants should be written | |
| Optional Parameters | |||
| --annotation -A |
[] | One or more specific annotations to apply to variant calls | |
| --excludeAnnotation -XA |
[] | One or more specific annotations to exclude | |
| --expression -E |
{} | One or more specific expressions to apply to variant calls | |
| --group -G |
[] | One or more classes/groups of annotations to apply to variant calls | |
| --MendelViolationGenotypeQualityThreshold -mvq |
0.0 | GQ threshold for annotating MV ratio | |
| Optional Flags | |||
| --alwaysAppendDbsnpId |
false | Add dbSNP ID even if one is already present | |
| --list -ls |
false | List the available annotations and exit | |
| --resourceAlleleConcordance -rac |
false | Check for allele concordances when using an external resource VCF file | |
| --useAllAnnotations -all |
false | Use all possible annotations (not for the faint of heart) | |
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 dbSNP ID even if one is already present
By default, a dbSNP ID is added only when the ID field in the variant record is empty (not already annotated).
This argument allows you to override that behavior, and appends the new ID to the existing one. This is used
in conjunction with the -dbsnp argument.
Boolean false
One or more specific annotations to apply to variant calls
See the --list argument to view available annotations.
List[String] []
Comparison VCF file
If a record in the 'variant' track 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).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
List[RodBinding[VariantContext]] []
dbSNP file
rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
One or more specific annotations to exclude
Note that this argument has higher priority than the -A or -G arguments,
so annotations will be excluded even if they are explicitly included with the other options.
List[String] []
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] {}
One or more classes/groups of annotations to apply to variant calls
If specified, all available annotations in the group will be applied. See the VariantAnnotator -list argument
to view available groups. Keep in mind that RODRequiringAnnotations are not intended to be used as a group,
because they require specific ROD inputs.
List[String] []
List the available annotations and exit
Note that the --list argument requires a fully resolved and correct command-line to work. As an alternative,
you can use ListAnnotations (see Help Utilities).
Boolean false
GQ threshold for annotating MV ratio
The genotype quality (GQ) threshold above which the mendelian violation ratio should be annotated.
double 0.0 [ [ -∞ ∞ ] ]
File to which variants should be written
VariantContextWriter stdout
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 --resourceAlleleConcordance, otherwise
the match is based on position only.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
List[RodBinding[VariantContext]] []
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
SnpEff file from which to get annotations
The INFO field will be annotated with information on the most biologically significant effect
listed for each variant in the SnpEff file.
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
RodBinding[VariantContext] none
Use all possible annotations (not for the faint of heart)
You can use the -XL 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 actually 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
Input VCF file
Variants from this VCF file are used by this tool as input.
The file must at least contain the standard VCF header lines, but
can be empty (i.e., no variants are contained in the file).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA