Do we need to normalize GIAB NA12878 high-conf vcf?
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Can you elaborate on what 'vt normalize' is actually doing? If neither you nor your colleague know, then perhaps the best thing to do is to find out why it may be needed on any VCF, and then to decide if it's needed for 'GIAB NA12878' by inspecting the structure of the variant calls in this particular file.
Thanks for you apply, I think I asked a stupid question after reading this link.... https://genome.sph.umich.edu/wiki/Variant_Normalization, and I will agree with my colleague, just in case that GIAB NA12878 have multi allele representations.
I see, yes, depending on your downstream analysis, it can be good practice to split multi-allelic calls into multiple variants. I normalise every VCF/BCF that passes through my fingers, just so that each is starting from the same state of normalisation (minimises issues later on).