Package org.snpeff.vcf


package org.snpeff.vcf
  • Class
    Description
    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
    Index a file that has "chr \t pos" as the beginning of a line (e.g.
    A simple chr:pos parser Stores using bytes instead of chars
    A pedigree for cancer samples
    Pedigree entry in a VCF file header E.g.: ##PEDIGREE=<Derived=Patient_01_Somatic,Original=Patient_01_Germline> or ##PEDIGREE=<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=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP.
    An 'CSQ' entry in a vcf header line
    An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
    A VCF entry (a line) in a VCF file
     
    A VCF genotype field There is one genotype per sample in each VCF entry
    Represents 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-41
     
    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=<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 line
    An 'NMD' entry in a vcf line