VEP Installconfiguration

S3 버킷에서 해당 json파일 객체를 선택하고 Copy S3 URI를 클릭합니다.

예시) vep-configuration-GRCh37.json

{
        "command": [
                "/opt/ensembl-vep/vep",
                "--format", "vcf",
                "--dir_plugins", "/opt/vep/plugins",
                "--dir_cache", "/opt/vep/cache",
                "--json",
                "--everything",
                "--allele_number",
                "--no_stats",
                "--cache", "--offline",
                "--minimal",
                "--assembly", "GRCh37",
                "--plugin", "LoF,human_ancestor_fa:/opt/vep/loftee_data/human_ancestor.fa.gz,filter_position:0.05,min_intron_size:15,conservation_file:/opt/vep/loftee_data/phylocsf_gerp.sql,gerp_file:/opt/vep/loftee_data/GERP_scores.final.sorted.txt.gz",
                "-o", "STDOUT"
        ],
        "env": {
                "PERL5LIB": "/opt/vep"
        },
    "vep_json_schema": "Struct{assembly_name:String,allele_string:String,ancestral:String,colocated_variants:Array[Struct{aa_allele:String,aa_maf:Float64,afr_allele:String,afr_maf:Float64,allele_string:String,amr_allele:String,amr_maf:Float64,clin_sig:Array[String],end:Int32,eas_allele:String,eas_maf:Float64,ea_allele:String,ea_maf:Float64,eur_allele:String,eur_maf:Float64,exac_adj_allele:String,exac_adj_maf:Float64,exac_allele:String,exac_afr_allele:String,exac_afr_maf:Float64,exac_amr_allele:String,exac_amr_maf:Float64,exac_eas_allele:String,exac_eas_maf:Float64,exac_fin_allele:String,exac_fin_maf:Float64,exac_maf:Float64,exac_nfe_allele:String,exac_nfe_maf:Float64,exac_oth_allele:String,exac_oth_maf:Float64,exac_sas_allele:String,exac_sas_maf:Float64,id:String,minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,somatic:Int32,start:Int32,strand:Int32}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,consequence_terms:Array[String],high_inf_pos:String,impact:String,minimised:Int32,motif_feature_id:String,motif_name:String,motif_pos:Int32,motif_score_change:Float64,strand:Int32,variant_allele:String}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String}],seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,canonical:Int32,ccds:String,cdna_start:Int32,cdna_end:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,domains:Array[Struct{db:String,name:String}],exon:String,gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,minimised:Int32,polyphen_prediction:String,polyphen_score:Float64,protein_end:Int32,protein_start:Int32,protein_id:String,sift_prediction:String,sift_score:Float64,strand:Int32,swissprot:String,transcript_id:String,trembl:String,tsl:Int32,uniparc:String,variant_allele:String}],variant_class:String}"
}

:코드에서 아래 내용에서 위에서 복사한 S3 객체 URI로 수정하여 사용할 수 있습니다.

VEP 플러그인 설치

만일 VEP의 플러그인 설치에 변경사항 (추가 등)이 있다면 AMI를 다시 만들어야 합니다. 이 때 AMI를 만들 데 사용되는 VEP 데이터설치에 다운로드관한 코드는  입니다. 해당 코드를 수정 후 다시 AMI를 빌드합니다.

다음을 참고하여 커스텀하게 Hail, VEP 툴을 설치 및 준비AMI를 방법을빌드할 설명