# Uses of Package
org.snpeff.snpEffect

Packages that use org.snpeff.snpEffect
Package
Description
org.snpeff
org.snpeff.binseq
org.snpeff.coverage
org.snpeff.filter
org.snpeff.interval
org.snpeff.interval.codonChange
org.snpeff.motif
org.snpeff.nextProt
org.snpeff.outputFormatter
org.snpeff.pdb
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.factory
org.snpeff.spliceSites
org.snpeff.stats
org.snpeff.svg
org.snpeff.util
org.snpeff.vcf

Classes in org.snpeff.snpEffect used by org.snpeff
Class
Description
Config
Classes in org.snpeff.snpEffect used by org.snpeff.binseq
Class
Description
Config
Classes in org.snpeff.snpEffect used by org.snpeff.coverage
Class
Description
SnpEffectPredictor
Predicts effects of SNPs
Classes in org.snpeff.snpEffect used by org.snpeff.filter
Class
Description
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
VariantEffect
Effect of a variant.
Classes in org.snpeff.snpEffect used by org.snpeff.interval
Class
Description
Config
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
ErrorWarningType
Errors and warnings
VariantEffect
Effect of a variant.
VariantEffects
A sorted collection of variant effects
Classes in org.snpeff.snpEffect used by org.snpeff.interval.codonChange
Class
Description
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
VariantEffect
Effect of a variant.
VariantEffect.EffectImpact
VariantEffects
A sorted collection of variant effects
Classes in org.snpeff.snpEffect used by org.snpeff.motif
Class
Description
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
Classes in org.snpeff.snpEffect used by org.snpeff.nextProt
Class
Description
Config
Classes in org.snpeff.snpEffect used by org.snpeff.outputFormatter
Class
Description
Config
VariantEffect
Effect of a variant.
Classes in org.snpeff.snpEffect used by org.snpeff.pdb
Class
Description
Config
Classes in org.snpeff.snpEffect used by org.snpeff.snpEffect
Class
Description
Config
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
ErrorWarningType
Errors and warnings
Hgvs
HGSV notation References: http://www.hgvs.org/
SnpEffectPredictor
Predicts effects of SNPs
VariantEffect
Effect of a variant.
VariantEffect.Coding
VariantEffect.EffectImpact
VariantEffect.FunctionalClass
This class is only getFused for SNPs
VariantEffects
A sorted collection of variant effects
VariantEffectStructural
Effect of a structural variant affecting multiple genes
VcfAnnotator
Annotate a VCF file: E.g.
Classes in org.snpeff.snpEffect used by org.snpeff.snpEffect.commandLine
Class
Description
Config
VcfAnnotator
Annotate a VCF file: E.g.
Classes in org.snpeff.snpEffect used by org.snpeff.snpEffect.factory
Class
Description
Config
SnpEffectPredictor
Predicts effects of SNPs
Classes in org.snpeff.snpEffect used by org.snpeff.spliceSites
Class
Description
Config
Classes in org.snpeff.snpEffect used by org.snpeff.stats
Class
Description
SnpEffectPredictor
Predicts effects of SNPs
VariantEffect
Effect of a variant.
Classes in org.snpeff.snpEffect used by org.snpeff.svg
Class
Description
SnpEffectPredictor
Predicts effects of SNPs
Classes in org.snpeff.snpEffect used by org.snpeff.util
Class
Description
ErrorWarningType
Errors and warnings
Classes in org.snpeff.snpEffect used by org.snpeff.vcf
Class
Description
EffectType
Effect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).
VariantEffect
Effect of a variant.
VariantEffect.Coding
VariantEffect.EffectImpact
VariantEffect.FunctionalClass
This class is only getFused for SNPs