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VariantFiltration

Filters variant calls using a number of user-selectable, parameterizable criteria.

Category Variant Evaluation and Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

VariantFiltration is a GATK tool for hard-filtering variant calls based on certain criteria. Records are hard-filtered by changing the value in the FILTER field to something other than PASS.

Input

A variant set to filter.

Output

A filtered VCF.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T VariantFiltration \
   -o output.vcf \
   --variant input.vcf \
   --filterExpression "AB < 0.2 || MQ0 > 50" \
   --filterName "Nov09filters" \
   --mask mask.vcf \
   --maskName InDel

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by VariantFiltration.

Window size

This tool uses a sliding window on the reference.

  • Window start: -50 bp before the locus
  • Window stop: 50 bp after the locus

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

VariantFiltration specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name Type Default value Summary
Required
--variant RodBinding[VariantContext] NA Input VCF file
Optional
--clusterSize Integer 3 The number of SNPs which make up a cluster
--clusterWindowSize Integer 0 The window size (in bases) in which to evaluate clustered SNPs
--filterExpression ArrayList[String] [] One or more expression used with INFO fields to filter
--filterName ArrayList[String] [] Names to use for the list of filters
--filterNotInMask boolean false Filter records NOT in given input mask.
--genotypeFilterExpression ArrayList[String] [] One or more expression used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)
--genotypeFilterName ArrayList[String] [] 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
--invalidatePreviousFilters boolean false Remove previous filters applied to the VCF
--mask RodBinding[Feature] none Input ROD mask
--maskExtension Integer 0 How many bases beyond records from a provided 'mask' rod should variants be filtered
--maskName String Mask The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call
--missingValuesInExpressionsShouldEvaluateAsFailing Boolean false When evaluating the JEXL expressions, missing values should be considered failing the expression
--out VariantContextWriter stdout File to which variants should be written

Argument details

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.

--clusterSize / -cluster ( Integer with default value 3 )

The number of SNPs which make up a cluster. Works together with the --clusterWindowSize argument.

--clusterWindowSize / -window ( Integer with default value 0 )

The window size (in bases) in which to evaluate clustered SNPs. Works together with the --clusterSize argument. To disable the clustered SNP filter, set this value to less than 1.

--filterExpression / -filter ( ArrayList[String] with default value [] )

One or more expression used with INFO fields to filter. VariantFiltration accepts any number of JEXL expressions (so you can have two named filters by using --filterName One --filterExpression "X < 1" --filterName Two --filterExpression "X > 2").

--filterName / -filterName ( ArrayList[String] with default value [] )

Names to use for the list of filters. This name is put in the FILTER field for variants that get filtered. Note that there must be a 1-to-1 mapping between filter expressions and filter names.

--filterNotInMask / -filterNotInMask ( boolean with default value false )

Filter records NOT in given input mask.. By default, if the -mask argument is used, any variant falling in a mask will be filtered. If this argument is used, logic is reversed, and variants falling outside a given mask will be filtered. Use case is, for example, if we have an interval list or BED file with "good" sites.

--genotypeFilterExpression / -G_filter ( ArrayList[String] with default value [] )

One or more expression used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info). Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead. VariantFiltration will add the sample-level FT tag to the FORMAT field of filtered samples (this does not affect the record's FILTER tag). One can filter normally based on most fields (e.g. "GQ < 5.0"), but the GT (genotype) field is an exception. We have put in convenience methods so that one can now filter out hets ("isHet == 1"), refs ("isHomRef == 1"), or homs ("isHomVar == 1").

--genotypeFilterName / -G_filterName ( ArrayList[String] with default value [] )

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. Similar to the INFO field based expressions, but used on the FORMAT (genotype) fields instead.

--invalidatePreviousFilters ( boolean with default value false )

Remove previous filters applied to the VCF. Invalidate previous filters applied to the VariantContext, applying only the filters here

--mask / -mask ( RodBinding[Feature] with default value none )

Input ROD mask. Any variant which overlaps entries from the provided mask rod will be filtered. If the user wants logic to be reversed, i.e. filter variants that do not overlap with provided mask, then argument -filterNotInMask can be used. --mask binds reference ordered data. This argument supports ROD files of the following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

--maskExtension / -maskExtend ( Integer with default value 0 )

How many bases beyond records from a provided 'mask' rod should variants be filtered.

--maskName / -maskName ( String with default value Mask )

The text to put in the FILTER field if a 'mask' rod is provided and overlaps with a variant call.

--missingValuesInExpressionsShouldEvaluateAsFailing ( Boolean with default value false )

When evaluating the JEXL expressions, missing values should be considered failing the expression. By default, if JEXL cannot evaluate your expression for a particular record because one of the annotations is not present, the whole expression evaluates as PASSing. Use this argument to have it evaluate as failing filters instead for these cases.

--out / -o ( VariantContextWriter with default value stdout )

File to which variants should be written.

--variant / -V ( required RodBinding[VariantContext] )

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). --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

See also Guide Index | Technical Documentation Index | Support Forum

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.