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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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ONE-BASED REFERENCE #1779

Open vappiah opened 4 weeks ago

vappiah commented 4 weeks ago

Dear Developers, I have my vcf file generated using UCSC HG38. I realized that is a zero-based coordinate system. I annotated the vcf with VEP and I also got to know that Ensemble uses a one-based .

Is the annotation information from VEP valid ? Or I have to call the variants using the ensemble genome before annotating?

Thanks

likhitha-surapaneni commented 3 weeks ago

Hi @vappiah , the specs of VCF (Variant Call Format) version 4.0 indicate 1-based coordinate system and VEP only supports this. Please let us know if this answers your question.