{ "command": [ "/opt/ensembl-vep/vep", "--format", "vcf", "__OUTPUT_FORMAT_FLAG__", "--hgvs", "--allele_number", "--no_stats", "--cache", "--dir_cache", "/opt/tutorials/var_db/reference", "--fields", "Allele,Consequence,Location,Gene", "--fasta", "/opt/tutorials/var_db/reference/hg38.fa", "--minimal", "--assembly", "GRCh38", "-o", "STDOUT" ], "env": {}, "vep_json_schema": "Struct {input: String,id: String,start: Int32,end: Int32,most_severe_consequence: String,allele_string: String,assembly_name: String,seq_region_name: String,strand: Int32,minimised: Int32,transcript_consequences: Array[Struct {transcript_id: String,gene_id: String,variant_allele: String,consequence_terms: Array[String],strand: Int32,distance: Int32,allele_num: Int32,flags: Array[String],hgvsc:String,hgvsp:String,hgvs_offset: Int32,impact: String,cdna_end: Int32,cdna_start: Int32,protein_start: Int32,protein_end: Int32,codons: String,cds_start: Int32,cds_end: Int32,amino_acids: String}],intergenic_consequences: Array[Struct {allele_num: Int32,consequence_terms: Array[String],impact: String,minimised: Int32,variant_allele: String}]}" }