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 genotypesRepresents 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
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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
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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
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Classes in org.snpeff.vcf used by org.snpeff.stats
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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 genotypesA 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