[ensembl-dev] VEP: TSL missing for refseq?

Will McLaren wm2 at ebi.ac.uk
Wed Nov 30 16:47:30 GMT 2016


Hi Ann,

TSL values are available only for Ensembl transcripts. The table you refer
to shows the NM identifier which has been mapped to the Ensembl transcript
by our xref (external references) pipeline. However, the database
containing the RefSeq transcripts themselves from which we build the VEP
cache does not contain the TSL values or mappings to them.

This view shows the RefSeq transcript as it exists in that database:

http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=otherfeatures;g=83715;r=1:6424788-6460944;t=NM_031475.2

Hope that's clear

Regards

Will McLaren
Ensembl Variation

On 30 November 2016 at 15:32, Black-Ziegelbein, Elizabeth A <
elizabeth-black at uiowa.edu> wrote:

> Good morning -
>
> I am using VEP v 84 , offline mode with caches and local fasta.  We were
> wanting to use RefSeq only.  We are specifying the —tsl flag – but I don’t
> see any values appearing in the TSL annotation field. When checking, I see
> TSL values that I would think should be appearing for our refseq
> transcripts … for example transcript NM_031475 – TSL1 value.
>
> Here is how I am running our local install of VEP v84:
>
> perl variant_effect_predictor.pl --offline --flag_pick_allele -pick_order
> rank,biotype,tsl,length --canonical --refseq --total_length --tsl --hgvs
> --dir_cache cache-dir/ --fasta Homo_sapiens.GRCh37.dna.primary_assembly.fa
> -i <myfile> --vcf -o <newfile> --stats_file <newstatsfile>
>
>
> Any thoughts on how I can get the TSL values for our refseq transcripts
> when running vep locally?
>
> Thanks so much!
>
> Ann Black-Ziegelbein
>
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