Hi all!
I'm dealing with vcf and tsv files always in the same scenario: unannotated_multisample-VCF and a related tsv with annotation(from VEP). I wonder in the possibility to request the output of VEP in VCF format but for now I have to write some custom-script for the task and the goal is to get an annotated vcf after mapping common positions from the two files ( the vcf and the tsv). I have inspect and used vcf2tsv ( does not work properly) and vcf-to-tab. But I think that is better to try a particular solution for this task.
Any kind of advice will be appreciated a lot.
This are the vcf fields (vcf format 4.2) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 100098_BM 100173-PB [...]
The tsv's ones: ID Chr Start End Ref Alt VQSR CohortAF VEP_Gene VEP_HGNC CanonicalTx Exonic_Func Trunc_Func Consequences ExonicFunc.ensGene ProteinPos AminoAcids Codons Damaged_Domains Damaged_Gene Damaged_Ensembl CLNSIG CLNDN AF AF_popmax AF_afr AF_sas AF_amr AF_eas AF_nfe AF_fin AF_asj Kor_AF KOVA_AF KRG1772_rare KRG1772_common KRG1772_indel SIFT_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred MutationAssessor_pred PROVEAN_pred MetaSVM_pred MetaLR_pred M-CAP_pred VEST3_score CADD_phred Eigen-raw
Using
--vcfflag you can tell VEP to output the results in VCF format.Ref: https://m.ensembl.org/info/docs/tools/vep/script/vep_options.html