domains / families / data / variant-normalization

variant-normalization

combined

Left-align and trim indels to parsimonious canonical form, decompose MNPs (atomize), and split multiallelic variants with bcftools norm. Use when comparing variants across callers or cohorts, preparing a VCF for database annotation or ClinVar/dbSNP matching, merging VCFs, reconciling vt-vs-bcftools representation discordance, or resolving the VCF-left-align vs HGVS-3'-rule clash.

When to use

• Normalize indel representation
• Split multiallelic variants
• Comparing variants from different callers
• Preparing VCF for downstream analysis
• Left-align indels
• Fixing reference alleles
• Atomize complex variants
• Remove duplicates after splitting

Skill page

Conflict

Both copies describe the same core task (normalizing VCF indels and splitting multiallelics with bcftools norm), but each contains material steps and constraints the other lacks. The first copy provides a broad, practical reference with many specific bcftools norm flags (-c modes, -d duplicate removal, -m+ join options, --atomize, --old-rec-tag) and Python cyvcf2 check scripts. The second copy provides the governing theoretical principle (parsimony + left-alignment), the explicit algorithm steps, version compatibility constraints, and a strong rationale for when normalization is mandatory. Crowning one would hide the other's unique, valuable content.