# Package org.snpeff.vcf

package org.snpeff.vcf

Related Packages
Package
Description
org.snpeff
Class
Description
EffFormatVersion
VcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation format
FileIndexChrPos
Index a file that has "chr \t pos" as the beginning of a line (e.g.
LineChrPos
A simple chr:pos parser Stores using bytes instead of chars
Pedigree
A pedigree for cancer samples
PedigreeEntry
Pedigree entry in a VCF file header E.g.: ##PEDIGREE=invalid input: '<'Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=invalid input: '<'Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
VariantVcfEntry
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.
VcfConsequence
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=invalid input: '<'ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP.
VcfConsequenceHeader
An 'CSQ' entry in a vcf header line
VcfEffect
An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
VcfEntry
A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes The VcfEntry represents the VCF line, NOT the variant itself.
VcfEntry.AlleleFrequencyType
VcfGenotype
A VCF genotype field There is one genotype per sample in each VCF entry
VcfHeader
Represents the header of a vcf file.
VcfHeaderEntry
Represents a info elements in a VCF file's header References: https://samtools.github.io/hts-specs/VCFv4.3.pdf http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
VcfHeaderFormat
VcfHeaderInfo
Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO=invalid input: '<'ID=ID,Number=number,Type=type,Description=description> Possible Types for INFO fields are: Integer, Float, Flag, Character, and String.
VcfHeaderInfo.VcfInfoNumber
Number of values in an INFO field.
VcfInfoType
VcfLof
An 'LOF' entry in a vcf line
VcfNmd
An 'NMD' entry in a vcf line