Hello,
I’m trying to annotate a matrix table with VEP. The table was from Manta VCF file. When I annotated deletions(SV) of which alleles was like ['ATGCATGC...ATGC', 'A']
, VEP was working well. The problem was the deletions that has alleles like ['A', '<DEL>']
was not annotated with VEP, therefore VEP results was NA
. But when I ran VEP without hail, strangely, there was no problem annotating that deletions.
I use hail 0.2.74, python 3.7.10, spark 3.1.1, VEP ver104.
Here is my vep-config.json. I use csq=True
option because of StructuralVariantOverlap
Plugin parsing error.
{
"command": [
"/home/a7420174/tools/ensembl-vep/vep",
"--format", "vcf",
"__OUTPUT_FORMAT_FLAG__",
"--everything",
"--no_stats", "--overlaps",
"--cache", "--offline",
"--assembly", "GRCh38",
"--per_gene", "--pick", "--pick_order", "canonical,appris,tsl,biotype,ccds,rank,length",
"--plugin", "StructuralVariantOverlap,file=/home/a7420174/WGS/ASD_WGS_SV/resources/nstd166.GRCh38.variant_call.vcf.gz,reciprocal=1,same_type=1",
"--nearest", "gene",
"-o", "STDOUT"
],
"env": {
"PERL5LIB": "/home/a7420174/perl5/lib/perl5:$PERL5LIB"
},
"vep_json_schema": "Struct{assembly_name:String,allele_string:String,ancestral:String,custom_annotations:Struct{gnomADg:Array[Struct{fields:Struct{AF:Float64,FILTER:String},allele:String,name:String}]},colocated_variants:Array[Struct{AA:String,AFR:String,AMR:String,EA:String,EAS:String,EUR:String,SAS:String,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],clin_sig_allele: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,gnomAD:String,gnomAD_AFR:String,gnomAD_AMR:String,gnomAD_ASJ:String,gnomAD_EAS:String,gnomAD_FIN:String,gnomAD_NFE:String,gnomAD_OTH:String,gnomAD_SAS:String,id:String,frequencies:Struct{G:Struct{eur:Float64,eas:Float64,amr:Float64,afr:Float64,sas:Float64}},minor_allele:String,minor_allele_freq:Float64,phenotype_or_disease:Int32,pubmed:Array[Int32],sas_allele:String,sas_maf:Float64,seq_region_name:String,somatic:Int32,start:Int32,strand:Int32,var_synonyms:String}],context:String,end:Int32,id:String,input:String,intergenic_consequences:Array[Struct{allele_num:Int32,cadd_raw:Float64,cadd_phred:Float64,consequence_terms:Array[String],impact:String,minimised:Int32,variant_allele:String,sv_overlap_name:String,bp_overlap:Int32,percentage_overlap:Float64,sv_overlap_pc:Int32,sv_overlap_af:Float64}],most_severe_consequence:String,motif_feature_consequences:Array[Struct{allele_num:Int32,cadd_phred:Float64,cadd_raw:Float64,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,transcription_factors:Array[String],variant_allele:String,sv_overlap_name:String,bp_overlap:Int32,percentage_overlap:Float64,sv_overlap_pc:Int32,sv_overlap_af:Float64}],regulatory_feature_consequences:Array[Struct{allele_num:Int32,biotype:String,cadd_raw:Float64,cadd_phred:Float64,consequence_terms:Array[String],impact:String,minimised:Int32,regulatory_feature_id:String,variant_allele:String,sv_overlap_name:String,bp_overlap:Int32,percentage_overlap:Float64,sv_overlap_pc:Int32,sv_overlap_af:Float64}],seq_region_name:String,nearest:Array[String],start:Int32,strand:Int32,transcript_consequences:Array[Struct{allele_num:Int32,amino_acids:String,appris:String,biotype:String,cadd_phred:Float64,cadd_raw:Float64,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,flags:Array[String],cds_end_NF:Array[String],gene_id:String,gene_pheno:Int32,gene_symbol:String,gene_symbol_source:String,hgnc_id:String,hgvsg:String,hgvsc:String,hgvsp:String,hgvs_offset:Int32,impact:String,intron:String,lof:String,lof_flags:String,lof_filter:String,lof_info:String,mane: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:Array[String],transcript_id:String,trembl:Array[String],tsl:Int32,uniparc:Array[String],uniprot_isoform:Array[String],mane_select:String,variant_allele:String,sv_overlap_name:String,bp_overlap:Int32,percentage_overlap:Float64,sv_overlap_pc:Int32,sv_overlap_af:Float64}],variant_class:String}"
}
Is there any suggestion you can offer?
Thanks