java -jar GenomeAnalysisTK.jar

Category

Genome Variant Analysis

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Usage

java -jar GenomeAnalysisTK.jar -T VariantFiltration -R reference.fasta -o output.vcf --variant input.vcf --filterExpression "AB 50" --filterName "SomeFilterName"

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Manual

Argument name(s)	Default value	Summary
Required Inputs
--variant  -V	NA	Input VCF file
Optional Inputs
--mask	none	Input ROD mask
Optional Outputs
--out  -o	stdout	File to which variants should be written
Optional Parameters
--clusterSize  -cluster	3	The number of SNPs which make up a cluster
--clusterWindowSize  -window	0	The window size (in bases) in which to evaluate clustered SNPs
--filterExpression  -filter	[]	One or more expression used with INFO fields to filter
--filterName	[]	Names to use for the list of filters
--genotypeFilterExpression  -G_filter	[]	One or more expression used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)
--genotypeFilterName  -G_filterName	[]	Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered
--maskExtension  -maskExtend	0	How many bases beyond records from a provided 'mask' rod should variants be filtered
--maskName	Mask	The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call
Optional Flags
--filterNotInMask	false	Filter records NOT in given input mask.
--invalidatePreviousFilters	false	Remove previous filters applied to the VCF
--invertFilterExpression  -invfilter	false	Invert the selection criteria for --filterExpression
--invertGenotypeFilterExpression  -invG_filter	false	Invert the selection criteria for --genotypeFilterExpression
--missingValuesInExpressionsShouldEvaluateAsFailing	false	When evaluating the JEXL expressions, missing values should be considered failing the expression
--setFilteredGtToNocall	false	Set filtered genotypes to no-call

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