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

Black-Ziegelbein, Elizabeth A elizabeth-black at uiowa.edu
Wed Nov 30 15:32:51 GMT 2016


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>

[cid:6572CBAE-CE6D-40A1-AFAE-356E480CE7ED]

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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