org.broadinstitute.hellbender.tools.walkers.varianteval

Class VariantEvalArgumentCollection

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.varianteval.VariantEvalArgumentCollection

public class VariantEvalArgumentCollection
extends java.lang.Object

The collection of arguments for VariantEval

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VariantEvalArgumentCollection.StratifyingScale

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALL_FAMILY_NAME
static java.lang.String	ALL_SAMPLE_NAME
java.io.File	ancestralAlignmentsFile
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	comps
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	compsProvided The variant file(s) to compare against.
DbsnpArgumentCollection	dbsnp dbSNP comparison VCF.
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	evals The variant file(s) to evaluate.
FeatureInput<htsjdk.variant.variantcontext.VariantContext>	goldStandard Some analyses want to count overlap not with dbSNP (which is in general very open) but actually want to itemize their overlap specifically with a set of gold standard sites such as HapMap, OMNI, or the gold standard indels.
FeatureInput<htsjdk.tribble.Feature>	intervalsFile File containing tribble-readable features for the IntervalStratificiation
boolean	keepSitesWithAC0
FeatureInput<htsjdk.tribble.Feature>	knownCNVsFile File containing tribble-readable features containing known CNVs.
java.util.Set<java.lang.String>	knownNames List of feature tracks to be used for specifying "known" variants other than dbSNP.
double	mendelianViolationQualThreshold
boolean	mergeEvals If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying variant set, and evaluate the union of the results.
double	minPhaseQuality
java.util.List<java.lang.String>	modulesToUse See the -list argument to view available modules.
java.lang.Boolean	noStandardModules
java.lang.Boolean	noStandardStratifications
int	numSamplesFromArgument
GATKPath	pedigreeFile
PedigreeValidationType	pedigreeValidationType
int	ploidy
boolean	requireStrictAlleleMatch
java.util.Set<java.lang.String>	sampleExpressions
java.util.ArrayList<java.lang.String>	selectExps
java.util.ArrayList<java.lang.String>	selectNames
java.util.List<java.lang.String>	stratificationsToUse

Constructor Summary

Constructors

Constructor and Description
VariantEvalArgumentCollection()

Method Summary

Modifier and Type	Method and Description
VariantEvalArgumentCollection.StratifyingScale	getAFScale()
boolean	getCompAFStratifier()
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	getComps()
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	getCompsProvided()
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	getEvals()
java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	getFeatureInputsForDrivingVariants()
FeatureInput<htsjdk.variant.variantcontext.VariantContext>	getGoldStand()
FeatureInput<htsjdk.tribble.Feature>	getIntervalsFile()
FeatureInput<htsjdk.tribble.Feature>	getKnownCNVsFile()
double	getMendelianViolationQualThreshold()
int	getPloidy()
boolean	ignoreAC0Sites()
boolean	isMergeEvals()
void	setAFScale(VariantEvalArgumentCollection.StratifyingScale AFScale)
void	setUseCompAFStratifier(boolean useCompAFStratifier)

Methods inherited from class java.lang.Object

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

Field Detail

ALL_SAMPLE_NAME

public static final java.lang.String ALL_SAMPLE_NAME

See Also:

Constant Field Values

ALL_FAMILY_NAME

public static final java.lang.String ALL_FAMILY_NAME

See Also:

Constant Field Values

evals

@Argument(fullName="eval",
          shortName="eval",
          doc="Input evaluation file(s)",
          optional=false)
public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> evals

The variant file(s) to evaluate.

compsProvided

@Argument(fullName="comparison",
          shortName="comp",
          doc="Input comparison file(s)",
          optional=true)
public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> compsProvided

The variant file(s) to compare against.

comps

public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> comps

dbsnp

@ArgumentCollection
public DbsnpArgumentCollection dbsnp

dbSNP comparison VCF. By default, the dbSNP file is used to specify the set of "known" variants. Other sets can be specified with the -known-name (--known_names) argument.

goldStandard

@Argument(fullName="gold-standard",
          shortName="gold",
          doc="Evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison",
          optional=true)
public FeatureInput<htsjdk.variant.variantcontext.VariantContext> goldStandard

Some analyses want to count overlap not with dbSNP (which is in general very open) but actually want to itemize their overlap specifically with a set of gold standard sites such as HapMap, OMNI, or the gold standard indels. This argument provides a mechanism for communicating which file to use

selectExps

@Argument(shortName="select",
          doc="One or more stratifications to use when evaluating the data",
          optional=true)
public java.util.ArrayList<java.lang.String> selectExps

selectNames

@Argument(shortName="select-name",
          doc="Names to use for the list of stratifications (must be a 1-to-1 mapping)",
          optional=true)
public java.util.ArrayList<java.lang.String> selectNames

sampleExpressions

@Argument(fullName="sample",
          shortName="sn",
          doc="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context",
          optional=true)
public java.util.Set<java.lang.String> sampleExpressions

pedigreeFile

@Argument(fullName="pedigree",
          shortName="ped",
          doc="Pedigree file for determining the population \"founders\"",
          optional=true)
public GATKPath pedigreeFile

pedigreeValidationType

@Argument(fullName="pedigreeValidationType",
          shortName="pedValidationType",
          doc="The strictness for validating the pedigree.  Can be either STRICT or SILENT.  Default is STRICT",
          optional=true)
public PedigreeValidationType pedigreeValidationType

knownNames

@Argument(shortName="known-name",
          doc="Name of feature bindings containing variant sites that should be treated as known when splitting eval features into known and novel subsets",
          optional=true)
public java.util.Set<java.lang.String> knownNames

List of feature tracks to be used for specifying "known" variants other than dbSNP.

stratificationsToUse

@Argument(fullName="stratification-module",
          shortName="ST",
          doc="One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)",
          optional=true)
public java.util.List<java.lang.String> stratificationsToUse

noStandardStratifications

@Argument(fullName="do-not-use-all-standard-stratifications",
          shortName="no-st",
          doc="Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)",
          optional=true)
public java.lang.Boolean noStandardStratifications

modulesToUse

@Argument(fullName="eval-module",
          shortName="EV",
          doc="One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -no-ev is specified)",
          optional=true)
public java.util.List<java.lang.String> modulesToUse

See the -list argument to view available modules.

noStandardModules

@Argument(fullName="do-not-use-all-standard-modules",
          shortName="no-ev",
          doc="Do not use the standard modules by default (instead, only those that are specified with the -EV option)",
          optional=true)
public java.lang.Boolean noStandardModules

minPhaseQuality

@Argument(fullName="min-phase-quality",
          shortName="mpq",
          doc="Minimum phasing quality",
          optional=true)
public double minPhaseQuality

mendelianViolationQualThreshold

@Argument(shortName="mvq",
          fullName="mendelian-violation-qual-threshold",
          doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.",
          optional=true)
public double mendelianViolationQualThreshold

ploidy

@Argument(shortName="ploidy",
          fullName="sample-ploidy",
          doc="Per-sample ploidy (number of chromosomes per sample)",
          optional=true)
public int ploidy

ancestralAlignmentsFile

@Argument(fullName="ancestral-alignments",
          shortName="aa",
          doc="Fasta file with ancestral alleles",
          optional=true)
public java.io.File ancestralAlignmentsFile

requireStrictAlleleMatch

@Argument(fullName="require-strict-allele-match",
          shortName="strict",
          doc="If provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping",
          optional=true)
public boolean requireStrictAlleleMatch

keepSitesWithAC0

@Argument(fullName="keep-ac0",
          shortName="keep-ac0",
          doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes",
          optional=true)
public boolean keepSitesWithAC0

mergeEvals

@Argument(fullName="merge-evals",
          shortName="merge-evals",
          doc="If provided, all -eval tracks will be merged into a single eval track",
          optional=true)
public boolean mergeEvals

If true, VariantEval will treat -eval 1 -eval 2 as separate tracks from the same underlying variant set, and evaluate the union of the results. Useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.

intervalsFile

@Argument(fullName="strat-intervals",
          shortName="strat-intervals",
          doc="File containing tribble-readable features for the IntervalStratificiation",
          optional=true)
public FeatureInput<htsjdk.tribble.Feature> intervalsFile

File containing tribble-readable features for the IntervalStratificiation

knownCNVsFile

@Argument(fullName="known-cnvs",
          shortName="known-cnvs",
          doc="File containing tribble-readable features describing a known list of copy number variants",
          optional=true)
public FeatureInput<htsjdk.tribble.Feature> knownCNVsFile

File containing tribble-readable features containing known CNVs. For use with VariantSummary table.

numSamplesFromArgument

@Hidden
 @Argument(fullName="num-samples",
          doc="If provided, modules that track polymorphic sites will not require that a site have AC > 0 when the input eval has genotypes",
          optional=true)
public int numSamplesFromArgument

Constructor Detail

VariantEvalArgumentCollection

public VariantEvalArgumentCollection()

Method Detail

getFeatureInputsForDrivingVariants

public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> getFeatureInputsForDrivingVariants()

getKnownCNVsFile

public FeatureInput<htsjdk.tribble.Feature> getKnownCNVsFile()

getEvals

public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> getEvals()

getComps

public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> getComps()

ignoreAC0Sites

public boolean ignoreAC0Sites()

getGoldStand

public FeatureInput<htsjdk.variant.variantcontext.VariantContext> getGoldStand()

getCompsProvided

public java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> getCompsProvided()

isMergeEvals

public boolean isMergeEvals()

getPloidy

public int getPloidy()

getIntervalsFile

public FeatureInput<htsjdk.tribble.Feature> getIntervalsFile()

getMendelianViolationQualThreshold

public double getMendelianViolationQualThreshold()

getAFScale

public VariantEvalArgumentCollection.StratifyingScale getAFScale()

getCompAFStratifier

public boolean getCompAFStratifier()

setAFScale

public void setAFScale(VariantEvalArgumentCollection.StratifyingScale AFScale)

setUseCompAFStratifier

public void setUseCompAFStratifier(boolean useCompAFStratifier)