[ensembl-dev] Question about vep refseq cache version annotation with dbNSFP plugin.

[Will McLaren]

Hi Namchul,

The current version of the dbNSFP plugin does not work with the RefSeq
cache; this is because data is looked up on a key constructed from the
position, variant allele and Ensembl transcript ID, so will not work when
the input key contains the RefSeq transcript ID and not the Ensembl one.

If dbNSFP add the RefSeq transcript ID as a field in the data files, then
the plugin could use this as its key; until then the plugin will only work
with the Ensembl cache.

Regards

Will McLaren
Ensembl Variation

On 29 April 2015 at 02:38, namchul ghim <chulghim at gmail.com> wrote:

> my environment
>  release v79
>  latest vep
>  dbnsfp version - 2.9
>  reference - grch37
>
> dbNSFP plugin works at vep original cache version  very well.
> but, does not work at  refseq cache version..
>
> Why?
> my command is the following.
>
> perl /src/ensembl-tools/scripts/variant_effect_predictor/
> variant_effect_predictor.pl -i example_GRCh37.vcf --cache --offline
> --everything --force_overwrite --dir /cache/GRCh37 -o out.vcf --vcf
> --refseq --species homo_sapiens --xref_refseq --regulatory
> --flag_pick_allele  --buffer_size 5000 --fork 10  --hgvs --force --fasta
> /cache/GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa  --plugin
> dbNSFP,/cache/GRCh37/dbNSFP/dbNSFP.gz,ref,alt,aaref,aaalt,rs_dbSNP141,hg38_chr,hg38_pos,genename,Uniprot_acc,Uniprot_id,Uniprot_aapos,Interpro_domain,cds_strand,refcodon,SLR_test_statistic,codonpos,fold-degenerate,Ancestral_allele,Ensembl_geneid,Ensembl_transcriptid,aapos,aapos_SIFT,aapos_FATHMM,SIFT_score,SIFT_converted_rankscore,SIFT_pred,Polyphen2_HDIV_score,Polyphen2_HDIV_rankscore,Polyphen2_HDIV_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_rankscore,Polyphen2_HVAR_pred,LRT_score,LRT_converted_rankscore,LRT_pred,MutationTaster_score,MutationTaster_converted_rankscore,MutationTaster_pred,MutationAssessor_score,MutationAssessor_rankscore,MutationAssessor_pred,FATHMM_score,FATHMM_rankscore,FATHMM_pred,MetaSVM_score,MetaSVM_rankscore,MetaSVM_pred,MetaLR_score,MetaLR_rankscore,MetaLR_pred,Reliability_index,PROVEAN_score,PROVEAN_converted_rankscore,PROVEAN_pred,GERP++_NR,GERP++_RS,GERP++_RS_rankscore,phyloP46way_primate,phyloP46way_primate_rankscore,phyloP46way_placental,phyloP46way_placental_rankscore,phyloP100way_vertebrate,phyloP100way_vertebrate_rankscore,phastCons46way_primate,phastCons46way_primate_rankscore,phastCons46way_placental,phastCons46way_placental_rankscore,phastCons100way_vertebrate,phastCons100way_vertebrate_rankscore,SiPhy_29way_pi,SiPhy_29way_logOdds,SiPhy_29way_logOdds_rankscore,LRT_Omega,UniSNP_ids,1000Gp1_AC,1000Gp1_AF,1000Gp1_AFR_AC,1000Gp1_AFR_AF,1000Gp1_EUR_AC,1000Gp1_EUR_AF,1000Gp1_AMR_AC,1000Gp1_AMR_AF,1000Gp1_ASN_AC,1000Gp1_ASN_AF,ESP6500_AA_AF,ESP6500_EA_AF,ARIC5606_AA_AC,ARIC5606_AA_AF,ARIC5606_EA_AC,ARIC5606_EA_AF,ExAC_AC,ExAC_AF,ExAC_Adj_AC,ExAC_Adj_AF,ExAC_AFR_AC,ExAC_AFR_AF,ExAC_AMR_AC,ExAC_AMR_AF,ExAC_EAS_AC,ExAC_EAS_AF,ExAC_FIN_AC,ExAC_FIN_AF,ExAC_NFE_AC,ExAC_NFE_AF,ExAC_SAS_AC,ExAC_SAS_AF,clinvar_rs,clinvar_clnsig,clinvar_trait,COSMIC_ID,COSMIC_CNT
>
>
>
>
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