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Learn NGS Variant Calling: A Hands-on Bioinformatics Course
Rating: 4.5 out of 5(46 ratings)
142 students

Learn NGS Variant Calling: A Hands-on Bioinformatics Course

Learn end-to-end variant calling using Linux and R: From Raw NGS data to variants with visualization and interpretation
Created byRafiq Ur Rehman
Last updated 12/2025
English

What you'll learn

  • Understand the fundamentals of variant calling and its role in NGS data analysis.
  • Set up a Linux environment for bioinformatics using Windows or native systems.
  • Perform quality control and trimming of raw FASTQ sequencing data.
  • Align sequencing reads to a reference genome using industry-standard tools.
  • Use Samtools and FreeBayes to call SNPs and indels from aligned reads.
  • Filter and refine variant calls to ensure accuracy and reliability.
  • Visualize genomic variants using IGV (Integrative Genomics Viewer).
  • Analyze and interpret VCF files using R and essential bioinformatics packages.
  • Automate parts of the variant calling pipeline with shell scripting.
  • Gain hands-on experience with real NGS datasets and submit results as assignments.

Course content

8 sections • 20 lectures • 3h 24m total length

  • Introduction of Course4:20

Requirements

  • No prior programming or bioinformatics experience is required — this course is beginner-friendly.
  • A computer (Windows, macOS, or Linux) with at least 8GB RAM is recommended for smoother processing.
  • Stable internet connection for downloading tools and datasets.
  • Willingness to learn basic Linux commands (we’ll cover them step-by-step).
  • Interest in genomics, DNA sequencing, or data analysis.

Description

Become a Variant Calling Pro Using Linux and R – No Prior Experience Needed!

Unlock the secrets of the genome with hands-on training in variant calling! This course gives you practical skills to analyze next-generation sequencing (NGS) data using industry-standard tools like FreeBayes, Samtools, and R, all within a Linux environment. Whether you're a student, researcher, or clinician, this course empowers you to process FASTQ data, perform variant calling, visualize VCFs, and extract biological insights using open-source pipelines.

What You'll Learn:

  • Linux for Bioinformatics: Learn essential commands and file systems for data handling and tool usage.

  • NGS Variant Calling Basics: Understand confidence, quality metrics, and key concepts in variant analysis.

  • Pipeline Setup: Download datasets, prepare your analysis environment, and index genomes.

  • Data Preprocessing: Run FastQC, trim reads, align with BWA, and prepare BAM files.

  • Variant Calling with FreeBayes: Perform SNP and indel calling and filter low-quality variants.

  • Visualization and Interpretation: View variants in IGV and interpret biological impact.

  • R for Genomic Analysis: Set up R and use it to explore and visualize variant data.

  • Assignments and Quizzes: Test your knowledge with assessments after each section.

Who This Course Is For:

  • Biology & Medical Students: Learn NGS data analysis without needing advanced programming.

  • Researchers & Clinicians: Build reproducible pipelines for cancer genomics, rare diseases, and more.

  • Bioinformatics Enthusiasts: Transition into genomics with a complete beginner-to-advanced course.

  • Professionals in Biotech & Pharma: Strengthen your role in precision medicine and diagnostics.

Course Features:

  • Hands-on projects and real datasets

  • Assignments and quizzes after each section

  • Downloadable scripts and guides

  • Lifetime access and certificate of completion

No coding experience needed – just your interest in genomics and bioinformatics!

Who this course is for:

  • Biology and medical students who want to gain hands-on skills in next-generation sequencing (NGS) and variant analysis.
  • Researchers and lab professionals looking to analyze genomic data independently without relying on a bioinformatics team.
  • Beginner bioinformaticians who want to build their first variant calling pipeline using Linux and R.
  • Healthcare and biotech professionals seeking to understand variant data for clinical genomics, diagnostics, or personalized medicine.
  • Educators and instructors who want a complete, ready-to-teach variant calling workflow for academic or training purposes.
  • Anyone curious about how DNA variants are discovered, filtered, visualized, and interpreted from raw sequencing data.

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