Category

Genome Variant Analysis


Usage

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


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Inputs
--comp
[]Comparison VCF file
--dbsnp
 -D
nonedbSNP file
--resource
[]External resource VCF file
--snpEffFile
noneSnpEff file from which to get annotations
Optional Outputs
--out
 -o
stdoutFile 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
0.0GQ threshold for annotating MV ratio
Optional Flags
--alwaysAppendDbsnpId
falseAdd dbSNP ID even if one is already present
--list
 -ls
falseList the available annotations and exit
--resourceAlleleConcordance
 -rac
falseCheck for allele concordances when using an external resource VCF file
--useAllAnnotations
 -all
falseUse all possible annotations (not for the faint of heart)


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