VCF INFO header lines
##SnpEffVersion="4.2 (build 2015-12-05)"
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele |
Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID |
Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length
| AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##VEP="v96" time="2019-05-14 17:42:50" cache="/opt/vep/.vep/homo_sapiens/96_GRCh38"
ensembl=96.7a35428 ensembl-funcgen=96.9c3a0cd ensembl-variation=96.70d2777 ensembl-io=96.6e65b30
1000genomes="phase3" COSMIC="87" ClinVar="201901" ESP="V2-SSA137" HGMD-PUBLIC="20184"
assembly="GRCh38.p12" dbSNP="151" gencode="GENCODE 30" genebuild="2014-07" gnomAD="r2.1"
polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP.
Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|
HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|
DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
##VEP="v101" time="2020-10-28 14:12:58" cache="/opt/vep/.vep/homo_sapiens/101_GRCh38"
ensembl-funcgen=101.b918a49 ensembl-io=101.943b6c2 ensembl=101.856c8e8 ensembl-variation=101.50e7372
1000genomes="phase3" COSMIC="90" ClinVar="202003" ESP="V2-SSA137" HGMD-PUBLIC="20194"
assembly="GRCh38.p13" dbSNP="153" gencode="GENCODE 35" genebuild="2014-07" gnomAD="r2.1"
polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP.
Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|
HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|
DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
| bdg-formats |
Index |
snpEff 4.2 |
Index |
Ensembl VEP v96,v101 |
Notes |
alternateAllele |
0 |
Allele |
0 |
Allele |
|
effects |
1 |
Annotation |
1 |
Consequence |
|
impact |
2 |
Annotation_Impact |
2 |
IMPACT |
New field impact |
geneName |
3 |
Gene_Name |
3 |
SYMBOL |
|
geneId |
4 |
Gene_ID |
4 |
Gene |
|
featureType |
5 |
Feature_Type |
5 |
Feature_type |
|
featureId |
6 |
Feature_ID |
6 |
Feature |
|
biotype |
7 |
Transcript_BioType |
7 |
BIOTYPE |
|
rank, total |
8 |
Rank |
8 |
EXON |
Rank / total : Exon or Intron rank / total number of exons or introns; map to rank, total |
|
|
|
9 |
INTRON |
Map to rank, total |
transcriptHgvs |
9 |
HGVS.c |
10 |
HGVSc |
|
proteinHgvs |
10 |
HGVS.p |
11 |
HGVSp |
|
cdnaPosition, cdnaLength |
11 |
cDNA.pos / cDNA.length |
12 |
cDNA_position |
cDNA_position / (cDNA_len optional) : Position in cDNA and trancript's cDNA length (one based). |
codingSequencePosition, codingSequenceLength |
12 |
CDS.pos / CDS.length |
13 |
CDS_position |
CDS_position / (CDS_len optional): Position and number of coding bases (one based includes START and STOP codons). |
proteinPosition, proteinLength |
13 |
AA.pos / AA.length |
14 |
Protein_position |
Protein_position / (Protein_len optional): Position and number of AA (one based, including START, but not STOP). |
distance |
14 |
Distance |
18 |
Distance |
|
messages |
15 |
ERRORS / WARNINGS / INFO |
|
|
|
referenceProteinSequence, alternateProteinSequence |
|
|
15 |
Amino_acids |
Amino_acids : Reference and variant amino acids; new fields referenceProteinSequence, alternateProteinSequence |
referenceCodingSequence, alternateCodingSequence |
|
|
16 |
Codons |
Codons : Reference and variant codon sequence; new fields referenceCodingSequence, alternateCodingSequence |
|
|
|
17 |
Existing_variation |
Existing_variation : Identifier(s) of co-located known variants |
strand |
|
|
19 |
STRAND |
STRAND : Strand of the feature (1/-1); new field strand |
|
|
|
20 |
FLAGS |
FLAGS: Transcript quality flags |
|
|
|
21 |
SYMBOL_SOURCE |
|
|
|
|
22 |
HGNC_ID |
|