Course Live Advanced Dr. Omics Edu

Somatic Variant Calling in Cancer Genomics: A Hands-On DNA-Seq Pipeline

A hands-on crash course covering the complete somatic variant calling workflow from raw DNA-Seq reads to variant identification, annotation, and cancer genomics interpretation.

  • 5.0/5
  • English
  • Updated Oct 2026
INR

₹45000

₹60000 25% off
USD

$600

$700 14% off

Indian learners pay in INR; international learners are billed in USD.

Enroll for International Students

Paying from outside India? Use this link to complete your payment.

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Somatic Variant Calling in Cancer Genomics: A Hands-On DNA-Seq Pipeline

About this course

The Somatic Variant Calling in Cancer Genomics: A Hands-On DNA-Seq Pipeline at Dr. Omics Edu is a live, mentor-led online course in NGS and genomics data analysis. It is a hands-on DNA-seq pipeline built specifically for somatic variants in cancer. You learn on real biological data and finish with a genomics analysis taken from raw reads to interpreted results that you can show to an employer, a guide or an admissions panel.
In this course you move through somatic versus germline variants, dna-seq quality control and alignment and pre-processing steps before variant calling, then apply them in a hands-on project. The course runs live online across 1 module, so you can ask your mentor questions as you work. It is an advanced-level course, best suited to learners who already know the fundamentals.

What you will learn

• Somatic versus germline variants
• DNA-seq quality control and alignment
• Pre-processing steps before variant calling
• Calling somatic variants from tumour-normal pairs
• Filtering and annotating variants
• Interpreting cancer driver mutations
Genomics data analyst, NGS bioinformatician, research associate, and a stronger profile for genomics research or higher studies.

Skills you will gain

Linux BWA SAMtools GATK Mutect2 ANNOVAR or VEP
Certification

Available

Issued by Dr. Omics Edu

Course curriculum

1 module

  • Day 1 – Introduction to cancer genomics workflows and the somatic variant calling pipeline overview.
  • Day 2 – Retrieving sequencing data from SRA (prefetch/fasterq-dump) and understanding tumor-normal pairs.
  • Day 3 – Quality control with FastQC and read trimming/adapter removal using fastp.
  • Day 4 – Reference genome basics (hg38) and indexing for alignment.
  • Day 5 – Read alignment to hg38 using BWA-MEM2 and SAM/BAM fundamentals.
  • Day 6 – Post-alignment cleanup: marking duplicates with Picard/GATK MarkDuplicates.
  • Day 7 – Introduction to somatic variant calling concepts and tumor-normal comparison logic.
  • Day 8 – Somatic variant calling with GATK Mutect2 (panel of normals, germline resource).
  • Day 9 – Variant filtering with FilterMutectCalls and understanding filter flags.
  • Day 10 – Orientation bias metrics and artifact filtering (LearnReadOrientationModel).
  • Day 11 – Variant annotation using VEP (Variant Effect Predictor) fundamentals.
  • Day 12 – Integrating oncogenic databases like CIViC for clinical relevance annotation.
  • Day 13 – Visual inspection of variants using IGV (Integrative Genomics Viewer).
  • Day 14 – Oncoplot visualizations and mutation landscape summaries using maftools.
  • Day 15 – Doubt session

What you need to start

  • Basic understanding of molecular biology and genetics.
  • Basic knowledge of DNA sequencing and NGS concepts is recommended.
  • Familiarity with the Linux command line is helpful but not mandatory.
  • Basic computer skills.
  • No prior experience in somatic variant calling is required.

Who this course is for

  • B.Sc, M.Sc, B.Tech, M.Tech and PhD students in biotechnology, genetics, microbiology, biochemistry or life sciences, and early-career researchers.
INR

₹45000

₹60000 25% off
USD

$600

$700 14% off

Indian learners pay in INR; international learners are billed in USD.

Enroll for International Students

Paying from outside India? Use this link to complete your payment.

Make an Enquiry
Active batch
Open for enrolment
Variant Calling Pipeline: A DNA-Seq Approach
  • Starts 19 Oct 2026
  • Ends 06 Nov 2026
  • Timing 7:00 PM – 8:00 PM
  • Days Mon, Tue, Wed, Thu, Fri
  • Platform MS Teams
This course includes
  • Format Live
  • Level Advanced
  • Language English
  • Modules 1
  • Certificate Yes
  • Provider Dr. Omics Edu
  • Live
  • instructor-led interactive training.
  • Hands-on somatic variant calling exercises.
  • Practical analysis of representative cancer DNA-Seq datasets.
  • Step-by-step guidance through the DNA-Seq pipeline.
  • Exposure to commonly used bioinformatics tools and workflows.
  • Supporting datasets and learning resources.
  • Course materials for reference and practice.
  • Certificate of participation/completion as applicable.
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