# Uses of Package
org.snpeff.vcf

Packages that use org.snpeff.vcf
Package
Description
org.snpeff.fileIterator
org.snpeff.genotypes
org.snpeff.outputFormatter
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.stats
org.snpeff.vcf

Classes in org.snpeff.vcf used by org.snpeff.fileIterator
Class
Description
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.
VcfHeader
Represents the header of a vcf file.
VcfInfoType
Classes in org.snpeff.vcf used by org.snpeff.genotypes
Class
Description
VcfGenotype
A VCF genotype field There is one genotype per sample in each VCF entry
Classes in org.snpeff.vcf used by org.snpeff.outputFormatter
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
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.
Classes in org.snpeff.vcf used by org.snpeff.snpEffect
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
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.
Classes in org.snpeff.vcf used by org.snpeff.snpEffect.commandLine
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
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.
Classes in org.snpeff.vcf used by org.snpeff.stats
Class
Description
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An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *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.
Classes in org.snpeff.vcf used by org.snpeff.vcf
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.LineAndPos
A line and the position on the file where it begins
LineChrPos
A simple chr:pos parser Stores using bytes instead of chars
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