org.broadinstitute.hellbender.tools.walkers.variantutils

Class ValidateVariants

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.VariantWalkerBase

org.broadinstitute.hellbender.engine.VariantWalker

org.broadinstitute.hellbender.tools.walkers.variantutils.ValidateVariants

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class ValidateVariants
extends VariantWalker

Validate a VCF file with a strict set of criteria

This tool is designed to validate the adherence of a file to VCF format. The tool will validate .g.vcf GVCF format files as well. For VCF specifications, see https://samtools.github.io/hts-specs/. Besides standard adherence to the VCF specification, this tool performs additional strict validations to ensure that the information contained within the file is correctly encoded. These include:

• REF - correctness of the reference base(s)
• CHR_COUNTS - accuracy of AC and AN values
• IDS - tests against rsIDs when a dbSNP file is provided (requires a dbsnp VCF provided via `--dbsnp`).
• ALLELES - that all alternate alleles are present in at least one sample

By default the tool applies all the strict validations unless you indicate which one should be excluded using `--validation-type-to-exclude`. You can exclude as many types as you want. Furthermore, you can exclude all strict validations with the special code `ALL`. In this case the tool will only test for adherence to the VCF specification.

Input

A VCF file to validate.

Usage examples

Minimally validate a file for adherence to VCF format:

gatk ValidateVariants \ -V cohort.vcf.gz

Validate a GVCF for adherence to VCF format, including REF allele match:

gatk ValidateVariants \ -V sample.g.vcf.gz \ -R reference.fasta -gvcf

To perform VCF format and all strict validations:

 gatk ValidateVariants \
   -R ref.fasta \
   -V input.vcf \
   --dbsnp dbsnp.vcf
 

To perform only VCF format tests:

 gatk ValidateVariants
   -R ref.fasta \
   -V input.vcf \
   --validation-type-to-exclude ALL
 

To perform all validations except the strict `ALLELE` validation:

 gatk ValidateVariants \
   -R ref.fasta \
   -V input.vcf \
   --validation-type-to-exclude ALLELES \
   --dbsnp dbsnp.vcf
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ValidateVariants.ValidationType

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DO_NOT_VALIDATE_FILTERED_RECORDS
static java.lang.String	GVCF_VALIDATE

Fields inherited from class org.broadinstitute.hellbender.engine.VariantWalker

drivingVariantFile

Fields inherited from class org.broadinstitute.hellbender.engine.VariantWalkerBase

FEATURE_CACHE_LOOKAHEAD

Fields inherited from class org.broadinstitute.hellbender.engine.GATKTool

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
ValidateVariants()

Method Summary

Modifier and Type	Method and Description
void	apply(htsjdk.variant.variantcontext.VariantContext vc, ReadsContext readsContext, ReferenceContext ref, FeatureContext featureContext) Process an individual variant.
void	onTraversalStart() Operations performed just prior to the start of traversal.
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).

Methods inherited from class org.broadinstitute.hellbender.engine.VariantWalker

getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup

Methods inherited from class org.broadinstitute.hellbender.engine.VariantWalkerBase

getBestAvailableSequenceDictionary, getProgressMeterRecordLabel, makeVariantFilter, requiresFeatures, traverse

Methods inherited from class org.broadinstitute.hellbender.engine.GATKTool

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolkitShortName, getToolName, getTransformedReadStream, hasFeatures, hasIntervals, hasReads, hasReference, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReads, requiresReference, useVariantAnnotations

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

GVCF_VALIDATE

public static final java.lang.String GVCF_VALIDATE

See Also:

Constant Field Values

DO_NOT_VALIDATE_FILTERED_RECORDS

public static final java.lang.String DO_NOT_VALIDATE_FILTERED_RECORDS

See Also:

Constant Field Values

Constructor Detail

ValidateVariants

public ValidateVariants()

Method Detail

onTraversalStart

public void onTraversalStart()

Description copied from class: GATKTool

Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.

Overrides:

onTraversalStart in class GATKTool

apply

public void apply(htsjdk.variant.variantcontext.VariantContext vc,
                  ReadsContext readsContext,
                  ReferenceContext ref,
                  FeatureContext featureContext)

Description copied from class: VariantWalkerBase

Process an individual variant. Must be implemented by tool authors. In general, tool authors should simply stream their output from apply(), and maintain as little internal state as possible.

Specified by:

apply in class VariantWalkerBase

Parameters:

vc - Current variant being processed.

readsContext - Reads overlapping the current variant. Will be an empty, but non-null, context object if there is no backing source of reads data (in which case all queries on it will return an empty array/iterator)

ref - Reference bases spanning the current variant. Will be an empty, but non-null, context object if there is no backing source of reference data (in which case all queries on it will return an empty array/iterator). Can request extra bases of context around the current variant's interval by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current variant. Will be an empty, but non-null, context object if there is no backing source of Feature data (in which case all queries on it will return an empty List).

onTraversalSuccess

public java.lang.Object onTraversalSuccess()

Description copied from class: GATKTool

Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.

Overrides:

onTraversalSuccess in class GATKTool

Returns:

Object representing the traversal result, or null if a tool does not return a value