Normalization of VCF file

[celine-weng]

Hi,

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

Thank you

[nakib103]

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]

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