VEP_VCF-annotator

MK for Variant annotation using VEP

In this MK users can annotate VCF files using Variant Effect Predictor http://www.ensembl.org/info/docs/tools/vep/script/index.html

Its necessary to previously have installed VEP databases. The MK annotation will generate a TSV file having the biological information listed at the end.

For this MK:

targets/ VCF files to annotate

results/ TAB sep files with annotation

results/ summary of variants for each file

Annotations added:

1. Uploaded_variation : Identifier of uploaded variant
2. Location : Location of variant in standard coordinate format (chr:start or chr:start-end)
3. Allele : The variant allele used to calculate the consequence
4. Gene : Stable ID of affected gene
5. Feature : Stable ID of feature
6. Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature
7. Consequence : Consequence type
8. cDNA_position : Relative position of base pair in cDNA sequence
9. CDS_position : Relative position of base pair in coding sequence
10. Protein_position : Relative position of amino acid in protein
11. Amino_acids : Reference and variant amino acids
12. Codons : Reference and variant codon sequence
13. Existing_variation : Identifier(s) of co-located known variants
14. IMPACT : Subjective impact classification of consequence type
15. DISTANCE : Shortest distance from variant to transcript
16. STRAND : Strand of the feature (1/-1)
17. FLAGS : Transcript quality flags
18. PICK : Indicates if this consequence has been picked as the most severe
19. SYMBOL : Gene symbol (e.g. HGNC)
20. SYMBOL_SOURCE : Source of gene symbol
21. HGNC_ID : Stable identifer of HGNC gene symbol
22. CANONICAL : Indicates if transcript is canonical for this gene
23. SWISSPROT : UniProtKB/Swiss-Prot accession
24. TREMBL : UniProtKB/TrEMBL accession
25. UNIPARC : UniParc accession
26. GENE_PHENO : Indicates if gene is associated with a phenotype, disease or trait
27. SIFT : SIFT prediction and/or score
28. PolyPhen : PolyPhen prediction and/or score
29. EXON : Exon number(s) / total
30. INTRON : Intron number(s) / total
31. HGVSc : HGVS coding sequence name
32. HGVSp : HGVS protein sequence name
33. HGVS_OFFSET : Indicates by how many bases the HGVS notations for this variant have been shifted
34. AF : Frequency of existing variant in 1000 Genomes combined population
35. AFR_AF : Frequency of existing variant in 1000 Genomes combined African population
36. AMR_AF : Frequency of existing variant in 1000 Genomes combined American population
37. EAS_AF : Frequency of existing variant in 1000 Genomes combined East Asian population
38. EUR_AF : Frequency of existing variant in 1000 Genomes combined European population
39. SAS_AF : Frequency of existing variant in 1000 Genomes combined South Asian population
40. ExAC_AF : Frequency of existing variant in ExAC combined population
41. ExAC_Adj_AF : Adjusted frequency of existing variant in ExAC combined population
42. ExAC_AFR_AF : Frequency of existing variant in ExAC African/American population
43. ExAC_AMR_AF : Frequency of existing variant in ExAC American population
44. ExAC_EAS_AF : Frequency of existing variant in ExAC East Asian population
45. ExAC_FIN_AF : Frequency of existing variant in ExAC Finnish population
46. ExAC_NFE_AF : Frequency of existing variant in ExAC Non-Finnish European population
47. ExAC_OTH_AF : Frequency of existing variant in ExAC combined other combined populations
48. ExAC_SAS_AF : Frequency of existing variant in ExAC South Asian population
49. CLIN_SIG : ClinVar clinical significance of the dbSNP variant
50. SOMATIC : Somatic status of existing variant
51. PHENO : Indicates if existing variant(s) is associated with a phenotype, disease or trait; multiple values correspond to multiple variants
52. MOTIF_NAME : The source and identifier of a transcription factor binding profile (TFBP) aligned at this position
53. MOTIF_POS : The relative position of the variation in the aligned TFBP
54. HIGH_INF_POS : A flag indicating if the variant falls in a high information position of the TFBP
55. MOTIF_SCORE_CHANGE : The difference in motif score of the reference and variant sequences for the TFBP