Package org.snpeff.snpEffect
package org.snpeff.snpEffect
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ClassDescriptionEffect type: Note that effects are sorted (declared) by impact (highest to lowest putative impact).Errors and warningsHGSV notation References: http://www.hgvs.org/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.Coding change in HGVS notation (amino acid changes) References: http://www.hgvs.org/mutnomen/recs.htmlHistogram of integer numbersAnalyze if a set of effects are can create a "Loss Of Function" and "Nonsense mediated decays" effects.Analize purity changes in codons and amino acidsPredicts effects of SNPsEffect of a variant.This class is only getFused for SNPsEffect of a structural variant (fusion) affecting two genesA sorted collection of variant effectsEffect of a structural variant affecting multiple genesAnnotate a VCF file: E.g.Maintains a list of VcfAnnotators and applies them one by one in the specified order