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