VCF output
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description of each column of the results
Variation type: Annotated using Sequence Ontology terms. Multiple effects can be concatenated using '&'.
Putative_impact: A simple estimation of putative impact / deleteriousness : {HIGH, MODERATE, LOW, MODIFIER}
Gene Name: Common gene name (HGNC). Optional: use closest gene when the variant is "intergenic".
Gene ID: Gene ID.
Feature type: Which type of feature is in the next field (e.g. transcript, motif, miRNA, etc.).
Feature ID: Depending on the annotation, this may be: Transcript ID (preferably using version number), Motif ID, miRNA, ChipSeq peak, Histone mark, etc. Note: Some features
may not have ID (e.g. histone marks from custom Chip-Seq experiments may not have a unique ID).
Transcript biotype: The bare minimum is at least a description on whether the transcript is {"Coding", "Noncoding"}.
Rank / total: Exon or Intron rank / total number of exons or introns.
HGVS.c: Variant using HGVS notation (DNA level).
HGVS.p: If variant is coding, this field describes the variant using HGVS notation (Protein level).
cDNA_position / cDNA_len: Position in cDNA and trancript's cDNA length (one based).
CDS_position / CDS_len: Position and number of coding bases (one based includes START and STOP codons).
Protein_position / Protein_len: Position and number of AA (one based, including START, but not STOP).
Distance to feature: All items in this field are options, so the field could be empty.
Up/Downstream: Distance to first / last codon.
Intergenic: Distance to closest gene.
Distance to closest Intron boundary in exon (+/- up/downstream). If same, use positive number.
Distance to closest exon boundary in Intron (+/- up/downstream).
Distance to first base in MOTIF.
Distance to first base in miRNA.
Distance to exon-intron boundary in splice_site or splice_region.
ChipSeq peak: Distance to summit (or peak center).
Histone mark / Histone state: Distance to summit (or peak center).
Errors, Warnings or Information messages: Add errors, warnings or informative message that can affect annotation accuracy.
BnVIR
Brassica
napus variation information resource
————Bridging the genotype–phenotype gap to accelerate
mining candidate variation of traits in Brassica napus