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 Sep 2026
Somatic Variant Calling in Cancer Genomics: A Hands-On DNA-Seq Pipeline

About this course

Somatic Variant Calling in Cancer Genomics: A Hands-On DNA-Seq Pipeline is a practical, hands-on course designed to introduce participants to the computational analysis of DNA-Seq data for identifying somatic variants associated with cancer.

Participants will learn the key stages of a somatic variant calling workflow, beginning with raw FASTQ data quality assessment and preprocessing, followed by read alignment, post-alignment processing, variant calling, filtering, annotation, and interpretation. The course emphasizes understanding how computational pipelines transform sequencing data into biologically meaningful variant information.

Through guided practical exercises, participants will work with representative cancer DNA-Seq datasets and gain an understanding of commonly used tools, file formats, quality metrics, and variant interpretation approaches used in cancer genomics research.

What you will learn

Understand the fundamentals of somatic variant calling in cancer genomics.
Understand the complete DNA-Seq analysis workflow from raw FASTQ files to annotated variants.
Perform quality assessment and preprocessing of sequencing reads.
Align DNA-Seq reads to a reference genome.
Understand post-alignment processing and quality metrics.
Perform somatic variant calling using appropriate bioinformatics workflows.
Apply variant filtering and understand key variant quality parameters.
Annotate identified variants and interpret relevant genomic information.
Generate and interpret common variant analysis outputs.
Understand the challenges and considerations involved in cancer somatic variant analysis.

Skills you will gain

DNA-Seq Analysis Somatic Variant Calling Cancer Genomics FASTQ Quality Control Read Trimming Sequence Alignment SAM/BAM Processing Variant Calling Variant Filtering VCF Processing Variant Annotation Genomic Coordinates Reference Genome Handling Variant Interpretation Linux Command Line NGS Data Analysis
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

  • Undergraduate and postgraduate students in Bioinformatics, Biotechnology, Biochemistry, Genetics, Microbiology, Biology, and Life Sciences.
  • Bioinformatics and genomics students.
  • Research scholars and PhD students.
  • Researchers working with NGS and cancer genomics data.
  • Beginners interested in DNA-Seq and variant analysis.
  • Life-science professionals looking to develop practical cancer genomics skills.
INR

₹45000

₹60000 25% off
USD

$600

$700 14% off

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

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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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