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MubasherMohammed
MubasherMohammedCOMMUNITY
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wgs-prs

Converts whole-genome sequencing data into polygenic risk scores via nf-core/sarek and bcftools VCF QC.

Updated May 10, 2026
Search Tags:#bioinformatics#variant calling#whole-genome-sequencing#polygenic-risk-scores#vcf quality control
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill wgs-prs
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: wgs-prs
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/wgs-prs
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill wgs-prs

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires python3, nextflow, docker, singularity, bcftools, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the entire process of converting whole-genome sequencing data into polygenic risk scores, saving time and reducing the complexity of bioinformatics analysis.

Core Features & Use Cases

  • End-to-End Pipeline: Handles variant calling, VCF quality control, and polygenic risk score computation.
  • Flexible Input: Accepts both paired-end FASTQ files and pre-existing VCF files.
  • Use Case: Ideal for researchers who need to quickly analyze large sets of whole-genome sequencing data and obtain risk scores without manual processing.

Quick Start

Run the wgs-prs skill with the provided paired-end FASTQ files and sample ID.

Frequently Asked Questions about wgs-prs

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

FAQPage Schema
How do I calculate polygenic risk scores from whole-genome sequencing data?▼

You calculate polygenic risk scores from whole-genome sequencing data by running an automated pipeline that uses nf-core/sarek for variant calling, bcftools for VCF quality control, and a PRS catalog for risk computation.

Can I use pre-existing VCF files instead of raw FASTQ for polygenic risk score analysis?▼

Yes, you can use pre-existing VCF files for polygenic risk score analysis. The pipeline accepts both paired-end FASTQ files and pre-existing VCF files as flexible input for germline variant assessment.

Do I need Nextflow and Docker to run whole-genome sequencing variant calling pipelines?▼

Yes, you need Nextflow and either Docker or Singularity to run whole-genome sequencing variant calling pipelines. The workflow also requires Python3 and bcftools to execute the automated analysis.

What is the best way to automate VCF quality control for germline variant analysis?▼

The best way to automate VCF quality control for germline variant analysis is using a pipeline that integrates bcftools to process variant calls before computing polygenic risk scores from a catalog.

Does bcftools work with nf-core/sarek for whole-genome sequencing quality control?▼

Yes, bcftools works with nf-core/sarek for whole-genome sequencing quality control. The pipeline uses sarek for variant calling and bcftools to filter and validate the resulting VCF files.

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