Validates a VCF file with an extra strict set of criteria.
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:
--dbsnpas show in examples below.
By default it will apply all the strict validations unless you indicate which one you want you want to exclude
-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.
A variant set to validate using
--variant as shown below.
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
These Read Filters are automatically applied to the data by the Engine before processing by ValidateVariants.
This tool applies the following downsampling settings by default.
This tool uses a sliding window on the reference.
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).
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|
|NA||Input VCF file|
|NA||which validation type to exclude from a full strict validation|
||NA||skip validation on filtered records|
||NA||just emit warnings on errors instead of terminating the run at the first instance|
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.
skip validation on filtered records
By default, even filtered records are validated.
which validation type to exclude from a full strict validation
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).
just emit warnings on errors instead of terminating the run at the first instance
GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA