genomics-vcf-operations

Name: genomics-vcf-operations
Availability: InStock
Author: TianGzlab

Parse, classify, and filter VCF variants with QUAL and DP metrics.

155|26|Updated Mar 14, 2026

Search Tags:#filtering #genomics #statistics #variant analysis #vcf #bcftools

Ready to run

npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-vcf-operations

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: genomics-vcf-operations
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-vcf-operations
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-vcf-operations

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

This Skill automates complex VCF file manipulations and statistical analyses, which are typically time-consuming and error-prone when done manually or with intricate command-line tools.

Core Features & Use Cases

Variant Statistics: Mirrors bcftools stats for Ti/Tv ratio, variant type counts (SNP, INDEL, MNP, COMPLEX), and quality metrics.
Filtering: Apply filters based on QUAL score, Depth (DP), and other INFO fields.
VCF Merging: Combines multiple VCF files into a single, coherent file.
Use Case: Quickly filter a large VCF file to keep only high-quality PASS variants with a minimum depth of 10x, and then generate a summary report of the variants.

Quick Start

Run the genomics-vcf-operations skill to filter the input VCF file 'variants.vcf' keeping only variants with a minimum quality of 30.

Frequently Asked Questions about genomics-vcf-operations

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I filter a VCF file by quality score and depth?▼

To calculate the Ti/Tv ratio for VCF variant analysis, generate variant statistics that mirror bcftools stats. This process evaluates transition and transversion rates alongside quality metrics for genomic data.

How do I parse multi-allelic variants in a VCF file?▼

To parse multi-allelic variants in a VCF file, perform multi-allelic parsing and variant classification. This mechanism handles complex variant types, categorizing them as SNP, INDEL, MNP, or COMPLEX for accurate reporting.

Can I merge multiple VCF files into a single coherent file?▼

You can merge multiple VCF files into a single coherent file using VCF merging operations. This combines separate variant datasets while maintaining structural consistency for downstream genomic analysis.

Does this VCF filtering approach work like bcftools and GATK SelectVariants?▼

This VCF filtering approach mirrors bcftools statistics and GATK SelectVariants functionality. It replicates variant classification and filtering logic without requiring intricate command-line tool operations.

What is the best way to keep only PASS variants in a large VCF file?▼

The best way to keep only PASS variants in a large VCF file is applying filters based on QUAL, DP, and INFO fields. This generates a filtered dataset and a summary report of the remaining variants.