add check_ref and dont_skip (#781)

Author: bpblanken

v03_pipeline/var/vep_config/vep-GRCh38.json

@@ -2,10 +2,10 @@
   "command": [
     "bash",
     "-c",
-    "/vep --format vcf -json --hgvs --biotype --canonical --mane --numbers --minimal --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g"
+    "/vep --format vcf -json --hgvs --biotype --canonical --mane --numbers --minimal --allele_number --no_stats --cache --offline --assembly GRCh38 --fasta /opt/vep/.vep/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --check_ref --dont_skip --plugin LoF,loftee_path:/plugins,gerp_bigwig:/opt/vep/.vep/gerp_conservation_scores.homo_sapiens.GRCh38.bw,human_ancestor_fa:/opt/vep/.vep/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee.sql --plugin UTRAnnotator,file=/opt/vep/.vep/uORF_5UTR_GRCh38_PUBLIC.txt --plugin SpliceRegion,Extended --plugin AlphaMissense,file=/opt/vep/.vep/AlphaMissense_hg38.tsv.gz --dir_plugins /plugins -o STDOUT | sed s/5utr/fiveutr/g"
   ],
   "env": {
     "PERL5LIB": "/plugins"
   },
-  "vep_json_schema": "Struct{allele_string:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,ancestral:String,consequence_terms:Array[String],context:String,impact:String,variant_allele:String}],minimised:Int32,most_severe_consequence:String,seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,biotype:String,canonical:Int32,cdna_end:Int32,cdna_start:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,flags:String,gene_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,mane_select:String,mane_plus_clinical:String,protein_end:Int32,protein_start:Int32,strand:Int32,transcript_id:String,variant_allele:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,existing_inframe_oorfs: Int32,existing_outofframe_oorfs: Int32,existing_uorfs: Int32,fiveutr_consequence: String,fiveutr_annotation: Dict[String, Dict[String, String]],spliceregion: Array[String],am_pathogenicity: Float32,am_class: String}]}"
+  "vep_json_schema": "Struct{allele_string:String,check_ref:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,ancestral:String,consequence_terms:Array[String],context:String,impact:String,variant_allele:String}],minimised:Int32,most_severe_consequence:String,seq_region_name:String,start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,biotype:String,canonical:Int32,cdna_end:Int32,cdna_start:Int32,cds_end:Int32,cds_start:Int32,codons:String,consequence_terms:Array[String],distance:Int32,flags:String,gene_id:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,mane_select:String,mane_plus_clinical:String,protein_end:Int32,protein_start:Int32,strand:Int32,transcript_id:String,variant_allele:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,existing_inframe_oorfs: Int32,existing_outofframe_oorfs: Int32,existing_uorfs: Int32,fiveutr_consequence: String,fiveutr_annotation: Dict[String, Dict[String, String]],spliceregion: Array[String],am_pathogenicity: Float32,am_class: String}]}"
 }