Uses of Package
org.snpeff.vcf
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Classes in org.snpeff.vcf used by org.snpeff.akka.vcf Class Description VcfEntry A VCF entry (a line) in a VCF file -
Classes in org.snpeff.vcf used by org.snpeff.akka.vcfStr Class Description VcfEntry A VCF entry (a line) in a VCF file -
Classes in org.snpeff.vcf used by org.snpeff.fileIterator Class Description VcfEntry A VCF entry (a line) in a VCF fileVcfHeader 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 formatVcfEntry A VCF entry (a line) in a VCF file -
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 formatVcfEntry A VCF entry (a line) in a VCF file -
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 formatVcfEntry A VCF entry (a line) in a VCF file -
Classes in org.snpeff.vcf used by org.snpeff.snpEffect.commandLine.eff Class Description VcfEntry A VCF entry (a line) in a VCF file -
Classes in org.snpeff.vcf used by org.snpeff.snpEffect.testCases.integration 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 formatVcfEntry A VCF entry (a line) in a VCF file -
Classes in org.snpeff.vcf used by org.snpeff.snpEffect.testCases.unity 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 -
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Class Description VcfEffect An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *VcfEntry A VCF entry (a line) in a VCF file -
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 formatFileIndexChrPos.LineAndPos A line and the position on the file where it beginsLineChrPos A simple chr:pos parser Stores using bytes instead of charsPedigreeEnrty Pedigree entry in a VCF file header E.g.: ##PEDIGREE=or ##PEDIGREE= 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=VcfConsequenceHeader An 'CSQ' entry in a vcf header lineVcfEffect 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 (a line) in a VCF fileVcfEntry.AlleleFrequencyType VcfGenotype A VCF genotype field There is one genotype per sample in each VCF entryVcfHeader 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-41VcfHeaderFormat 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=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 lineVcfNmd An 'NMD' entry in a vcf line