# Package org.snpeff.snpEffect

package org.snpeff.snpEffect

Related Packages
Package
Description
org.snpeff
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.factory
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/
HgvsDna
Coding DNA reference sequence References http://www.hgvs.org/mutnomen/recs.html Nucleotide numbering: - there is no nucleotide 0 - nucleotide 1 is the A of the ATG-translation initiation codon - the nucleotide 5' of the ATG-translation initiation codon is -1, the previous -2, etc.
HgvsProtein
Coding change in HGVS notation (amino acid changes) References: http://www.hgvs.org/mutnomen/recs.html
IntHisto
Histogram of integer numbers
LossOfFunction
Analyze if a set of effects are can create a "Loss Of Function" and "Nonsense mediated decays" effects.
ProteinFastaWriter
Writes protein sequences to a FASTA file
PurityChange
Analize purity changes in codons and amino acids
SnpEffectPredictor
Predicts effects of SNPs
VariantEffect
Effect of a variant.
VariantEffect.Coding
VariantEffect.EffectImpact
VariantEffect.FunctionalClass
This class is only getFused for SNPs
VariantEffectFusion
Effect of a structural variant (fusion) affecting two genes
VariantEffects
A sorted collection of variant effects
VariantEffectStructural
Effect of a structural variant affecting multiple genes
VcfAnnotator
Annotate a VCF file: E.g.
VcfAnnotatorChain
Maintains a list of VcfAnnotators and applies them one by one in the specified order