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<div>Good morning -</div>
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<div>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. </div>
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<div>Here is how I am running our local install of VEP v84:</div>
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<span style="font-variant-ligatures: no-common-ligatures">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></span></p>
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<div>Any thoughts on how I can get the TSL values for our refseq transcripts when running vep locally?</div>
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<div>Thanks so much!</div>
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<div>Ann Black-Ziegelbein</div>
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