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

Thu Apr 30 14:16:08 BST 2015

Thanks a lot.
dev at ensembl.org  is very good mailing list to me

Regards

namchul

On Thu, Apr 30, 2015 at 9:23 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Namchul,
>
> Please take all of this with a pinch of salt; mappings between Ensembl and
> RefSeq transcripts vary in quality, and there is no guarantee that if a
> corresponding ID is found it will have the same transcript sequence
> (typically they will differ in non-coding regions but coding differences
> are also not uncommon).
>
> Any sequence differences will therefore make values calculated against
> Ensembl transcripts (such as those in dbNSFP) potentially invalid and
> misleading. Also bear in mind that the current dbNSFP release may use
> transcripts from an older version of Ensembl than is current for the VEP.
>
> On 30 April 2015 at 08:46, namchul ghim <chulghim at gmail.com> wrote:
>
>> Thanks..
>>
>> 1)
>>  I got grch39 mapping list (ensembl transcriptid and refseq_transcript
>> id) from your  homo_sapiens_core_79_38
>>
>> But, I can't homo_sapiens_core_79_37 database.
>> where do i get GRCh37 version's mapping list ?
>>
>
> You can connect to the 37 database on port 3337:
>
> mysql -hensembldb.ensembl.org -uanonymous -P3337 -Dhomo_sapiens_core_79_37
>
> You could also try BioMart to retrieve the mapping, e.g:
>
> http://grch37.ensembl.org/biomart/martview/b7985fa1a36be3b616c0b915031b9a1a
>
>
>>
>>
>> 2)  I will insert refseq id in dbNSFP db file.
>>      What is the field name ?
>>
>
> The field VEP uses in the dbNSFP file is named Ensembl_transcriptid. You
> could replace this with the RefSeq ID and use the plugin unmodified, but it
> would be better to add it as a new field and modify the plugin (just grep
> dbNSFP.pm for Ensembl_transcriptid to see where you need to change it).
>
> Regards
>
> Will
>
>
>>
>>
>>
>> On Wed, Apr 29, 2015 at 7:27 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>
>>> 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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