Tool for adding annotations to VCF files
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.
VariantAnnotator \ -R reference.fasta \ -I input.bam \ -V input.vcf \ -o output.vcf \ -A Coverage \ --dbsnp dbsnp.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
VariantAnnotator \ -R reference.fasta \ -V input.vcf \ -o output.vcf \ --resource foo:resource.vcf \ --expression foo.AF \ --expression foo.FILTER
This tool will not output every annotation as many cannot be made without computing the per-read AlleleLikelihoods, which is generated in either the HaplotypeCaller or Mutect2.
This tool outputs no annotations by default, all annotations/groups must be specified explicitly.
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.
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 |
null | The file to whcih variants should be written | |
| --variant -V |
null | 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 |
null | 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 | |
| --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. | |
| --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 | |
| --pedigree -ped |
null | Pedigree file for determining the population "founders" | |
| --reference -R |
null | 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 |
null | 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 | |
| --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 |
null | Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | |
| --tmp-dir |
null | 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 | |||
| --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 | |
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.
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
If true, adds a command line header line to created VCF files.
boolean true
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] []
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] []
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] []
read one or more arguments files and add them to the command line
List[File] []
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
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]] []
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
If true, create a a MD5 digest any VCF file created.
boolean false
dbSNP file
A dbSNP VCF file.
FeatureInput[VariantContext] null
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
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default annotations
Hook allowing for the user to remove default annotations from the tool
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
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
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] []
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] []
Samples representing the population "founders"
List[String] []
A configuration file to use with the GATK.
String null
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.
String ""
display the help message
boolean false
BAM/SAM/CRAM file containing reads
List[String] []
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 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:
IntervalMergingRule ALL
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 [ [ -∞ ∞ ] ]
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:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Lenient processing of VCF files
boolean false
The file to whcih variants should be written
R File null
Pedigree file for determining the population "founders"
File null
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
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[String] []
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:
ValidationStringency SILENT
Reference sequence
String null
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]] []
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
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
String null
display hidden arguments
boolean false
If true, don't emit genotype fields when writing vcf file output.
boolean false
Temp directory to use.
String null
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
A VCF file containing variants
R String null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.