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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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Normalization of VCF file #1647

Closed celine-weng closed 2 weeks ago

celine-weng commented 3 months ago

Hi,

Since my vcf file is left-normalized, do I need to conduct normalization before I process my file?

Thank you

nakib103 commented 3 months ago

Hi @celine-weng,

Thanks for your query!

If your variant is already left-normalized you might also look at minimising the alleles. This article is very helpful to understand this - https://genome.sph.umich.edu/wiki/Variant_Normalization

VEP does not minimise alleles by default but you can provide --minimise option to let VEP know to do this task for you (see here).

Hope that answers your query.

Best regards, Nakib

nakib103 commented 2 weeks ago

Hello @celine-weng, I will close this issue, if you face further problems please feel free to open a new one.