Hello, forgive my ignorance-
Suppose input.vcf contains a complex multiallelic site.
What is the difference between
bcftools norm --multiallelics -any -f hg38.fa input.vcf
bcftools norm --atomize -f hg38.fa input.vcf
I understand what
--multiallelics -any does but not sure what is going on with
--atomize. In the documentation it says "Decompose complex variants, e.g. split MNVs into consecutive SNVs.". I do not understand what this means for a multiallelic site.
If someone has a good example that would help clarify, that would be great.
Thanks in advance.