Tooluniverse Variant Analysis

This handles the full VCF analysis stack: parsing variant calls, annotating consequence types (synonymous, missense, frameshift), filtering by VAF, and splitting coding from non-coding variants. Ships with three battle-tested scripts that encode the gotchas you'd otherwise spend hours debugging. The GATK HaplotypeCaller pipeline script runs BWA alignment through variant calling or counts existing VCFs with proper multi-allelic split handling. The coding variant filter knows about two-row VarSeq Excel headers and correctly excludes intronic, intergenic, and UTR junk. The fraction calculator uses coding variants as the denominator, not all variants, which matters when clinical papers report mutation burdens. One heads-up: it defaults to diploid calling because that's what most published HaplotypeCaller runs used, even on prokaryotes.