bio-variant-normalization

Why Normalize?

The same variant can be represented multiple ways:

## bcftools norm

**Goal:** Left-align indels and check reference allele consistency.

**Approach:** Use bcftools norm with a reference FASTA to shift indels to the leftmost position and optionally fix/exclude REF mismatches.

**"Normalize my VCF before comparing callers"** → Left-align indel representations and split multiallelic sites for consistent variant comparison.

## Left-Align Indels

Requires reference FASTA to determine left-most representation.