genomics-variant-calling

Name: genomics-variant-calling
Availability: InStock
Author: TianGzlab

Call germline and somatic SNVs and Indels from SAM/BAM files to VCF.

155|26|Updated Mar 14, 2026

Search Tags:#genomics #vcf #indel #variant calling #gatk #deepvariant #snv

Ready to run

npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-variant-calling

💬 Prompt for ChatGPT / Claude Chat▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires GATK 4.x, samtools, bcftools, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the complex process of identifying genetic variations (SNVs, Indels) from genomic data, distinguishing true biological signals from technical noise.

Core Features & Use Cases

Variant Calling: Supports multiple leading callers like GATK HaplotypeCaller, Mutect2, and DeepVariant for both germline and somatic variants.
Quality Filtering: Implements VQSR or hard filtering to ensure high-quality variant calls.
Use Case: Analyze a whole-genome sequencing BAM file to identify all single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) present in the sample, preparing the data for downstream genomic analysis.

Quick Start

Call germline variants from the provided BAM file 'sample.bam' and save the results to the 'output_dir' directory.

Frequently Asked Questions about genomics-variant-calling

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

FAQPage Schema

How do I identify SNVs and Indels from a BAM file?▼

To perform germline variant calling, you use GATK HaplotypeCaller or DeepVariant to analyze SAM/BAM alignment files, generating a VCF output that lists all identified single nucleotide polymorphisms and insertions/deletions present in the sample.

What is the difference between germline and somatic variant calling?▼

Germline variant calling identifies inherited genetic variations using GATK HaplotypeCaller or DeepVariant, while somatic variant calling detects acquired tumor mutations using GATK Mutect2, both producing VCF outputs from SAM/BAM alignment files.

How do I apply VQSR and hard filtering for variant quality control?▼

Variant quality control applies VQSR or hard filtering to the initial VCF output to distinguish true biological genetic signals from technical sequencing noise, ensuring high-quality SNV and Indel variant calls for downstream analysis.

Does this variant calling workflow support the GVCF format?▼

Yes, the variant calling workflow includes a specific GVCF workflow utilizing GATK HaplotypeCaller to record both called and uncalled genomic sites, enabling accurate joint genotyping across multiple sequencing samples.

Can I use GATK Mutect2 and FreeBayes for somatic variant calling?▼

Yes, you can use GATK Mutect2 or FreeBayes for somatic variant calling. These tools analyze SAM/BAM alignment files to detect acquired somatic SNVs and Indels, generating a VCF output for downstream genomic analysis.

What is the best way to call variants from whole-genome sequencing data?▼

The best way to call variants from whole-genome sequencing data is using GATK HaplotypeCaller or DeepVariant to analyze BAM files, followed by VQSR or hard filtering for quality control to produce high-confidence VCF outputs.