genomics-variant-calling

name	genomics-variant-calling
description	Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split). Skip when filtering / merging VCFs (use `genomics-vcf-operations`), when calling structural variants (use `genomics-sv-detection`), or when adding functional annotations (use `genomics-variant-annotation`).
version	0.5.0
author	OmicsClaw
license	MIT
tags	["genomics","variant-calling","snv","indel","vcf","ti-tv"]
requires	["pandas","numpy"]

genomics-variant-calling

When to use

The user has a VCF (or a BAM intended for calling) and wants small-variant summary statistics: total variant count, SNP / indel split, Ti/Tv ratio, per-chromosome distribution. The script does invoke an external caller (GATK HaplotypeCaller, Mutect2, DeepVariant, FreeBayes, etc.) — it summarises an existing VCF or generates a demo VCF for downstream-skill smoke tests.