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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
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EGFR select NM_005228.5 but not NM_005228.3 #1061

Closed asmlgkj closed 2 years ago

asmlgkj commented 2 years ago

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System

in LRG, egfr select NM_005228.3, but vep is NM_005228.5, annovar is NM_005228.4, is there any select standards, <> it seems that .5 is the most updated in NCBI, how can I get all the newest NM minor version thanks a lot

dglemos commented 2 years ago

Hi @asmlgkj, The RefSeq transcripts available in VEP are imported from NCBI. We try to keep the data updated. To download the latest transcript IDs, you can use the file GFF or GTF file available here: https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/109.20210514/GCF_000001405.39_GRCh38.p13/

asmlgkj commented 2 years ago

thanks a lot @dglemos