Variant Normalization

Question

[spesks]

Is normalization is mandatory before merging vcfs? What will the merged file look like if the vcf samples were not pre-normalized? How will this affect further analysis?

Answer 1

[Istvan Albert]

The purpose of normalization is to ensure that identical variants are represented identically.

When not normalized, the same variants may be reported as different.

That being said the problem typically affects only a small subset of your variants but in those cases the problems will be systematic.