Documentation

ValidateVariants

Validates a VCF file with an extra strict set of criteria.

Category Validation Utilities

Traversal LocusWalker

PartitionBy LOCUS


Overview

ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it. In addition to standard adherence to the VCF specification, this tool performs extra strict validations to ensure the information contained within the file is correct. These include:

REF
the correctness of the reference base(s).
CHR_COUNTS
accuracy of AC & AN values.
IDS
tests against rsIDs when a dbSNP file is provided. Notice that for this one to work, you need to provide a reference to the dbsnp variant containing file using the --dbsnp as show in examples below.
ALLELES
and that all alternate alleles are present in at least one sample.

By default it will apply all the strict validations unless you indicate which one you want you want to exclude using -Xtype|--validationTypeToExclude <code>, where code is one of the listed above. You can exclude as many types as you want

Yo can exclude all strict validations with the special code ALL. In this case the tool will only test the adherence to the VCF specification.

Input

A variant set to validate using -V or --variant as shown below.

Examples

To perform VCF format and all strict validations:

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T ValidateVariants \
   --variant input.vcf \
   --dbsnp dbsnp.vcf
 

To perform only VCF format tests:

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T ValidateVariants \
   --validationTypeToExclude ALL \
   --variant input.vcf
 

To perform all validations except the strict ALLELE validation:

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T ValidateVariants \
   --validationTypeToExclude ALLELES
   --variant input.vcf \
   --dbsnp dbsnp.vcf
 

Additional Information

Read filters

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

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Window size

This tool uses a sliding window on the reference.

  • Window start: 0 bp before the locus
  • Window stop: 100 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).

ValidateVariants specific arguments

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 Inputs
--variant
 -V
NA Input VCF file
Optional Inputs
--dbsnp
 -D
none dbSNP file
Optional Parameters
--validationTypeToExclude
 -Xtype
[] which validation type to exclude from a full strict validation
Optional Flags
--doNotValidateFilteredRecords
false skip validation on filtered records
--warnOnErrors
false just emit warnings on errors instead of terminating the run at the first instance

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.


--dbsnp / -D

dbSNP file

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

RodBinding[VariantContext]  none


--doNotValidateFilteredRecords / -doNotValidateFilteredRecords

skip validation on filtered records
By default, even filtered records are validated.

Boolean  false


--validationTypeToExclude / -Xtype

which validation type to exclude from a full strict validation

List[ValidationType]  []


--variant / -V

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

R RodBinding[VariantContext]


--warnOnErrors / -warnOnErrors

just emit warnings on errors instead of terminating the run at the first instance

Boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA