Uses of Package
org.snpeff.vcf
Packages that use org.snpeff.vcf
Package
Description
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Classes in org.snpeff.vcf used by org.snpeff.fileIteratorClassDescriptionA 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.Represents the header of a vcf file.
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Classes in org.snpeff.vcf used by org.snpeff.genotypesClassDescriptionA VCF genotype field There is one genotype per sample in each VCF entry
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Classes in org.snpeff.vcf used by org.snpeff.outputFormatterClassDescriptionVcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation formatA 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.
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Classes in org.snpeff.vcf used by org.snpeff.snpEffectClassDescriptionVcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation formatA 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.
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Classes in org.snpeff.vcf used by org.snpeff.snpEffect.commandLineClassDescriptionVcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation formatA 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.
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Classes in org.snpeff.vcf used by org.snpeff.statsClassDescriptionAn 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *A VCF entry is a line in a VCF file A VCF line can have multiple variants, and multiple genotypes The VcfEntry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.
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Classes in org.snpeff.vcf used by org.snpeff.vcfClassDescriptionVcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation formatA line and the position on the file where it beginsA simple chr:pos parser Stores using bytes instead of charsPedigree 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>Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.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.An 'CSQ' entry in a vcf header lineAn '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) *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.A VCF genotype field There is one genotype per sample in each VCF entryRepresents the header of a vcf file.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-41Represents 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.Number of values in an INFO field.An 'LOF' entry in a vcf lineAn 'NMD' entry in a vcf line