ONE-BASED REFERENCE

[vappiah]

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]

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.