Clinical Exome Sequencing, Variant Calling, ACMG Interpretation & Pharmacogenomics (Online Workshop)

27-30 May 2026 | 6:30 PM IST | Online Hands-on Workshop | Certificate

About the Workshop

Step into the world of clinical genomics and precision medicine with this intensive 5-day online workshop focused on Clinical Exome Sequencing (WES), Variant Calling, ACMG Interpretation, and Pharmacogenomics. Participants will learn the complete workflow beginning from sequencing fundamentals and FASTQ data handling to alignment, variant calling, annotation, ACMG interpretation, and pharmacogenomic analysis.

What You Will Learn

• Fundamentals of genomics and Next-Generation Sequencing (NGS)

• Whole Exome Sequencing (WES) workflows

• Linux and command-line basics for bioinformatics

• Alignment using BWA-MEM

• GATK Best Practices pipeline

• Variant calling and filtering workflows

• Variant annotation using ANNOVAR

• ACMG guideline-based interpretation

• Pharmacogenomics and precision medicine concepts

Course Features

• Live interactive online workshop

• Hands-on practical sessions with real workflows

• Bioinformatics pipeline demonstrations

• Lecture recordings and study materials

• e-Certificate upon completion

Learning Outcomes

• Understand NGS and WES workflows

• Process FASTQ, BAM, and VCF files

• Perform alignment and variant calling using GATK workflows

• Annotate and interpret variants using ACMG guidelines

• Analyze pharmacogenomics and precision medicine datasets

• Understand clinical genomics reporting workflows

Who Can Join

• Biotechnology and Life Science students

• Research scholars and clinicians

• Bioinformatics beginners

• Healthcare professionals

• Anyone interested in genomics and precision medicine

  
  Course Fee

• Indian Participants: ₹1,800

• Previous CATR Participants: ₹1,500

• International Participants: $125 USD

• Previous International Participants: $100 USD

  
  Workshop Module
  

  Day 1 — Foundations of NGS and Sequencing Technologies

  Theme: How sequencing data is generated

  Session 1: Introduction to Genomics

  • DNA, genes, chromosomes

  • Exons vs introns

  • Central dogma

  • Genetic variants

  • SNP, SNV, Indels

  • Structural variants

  • Germline vs Somatic mutations

  Session 2: Next Generation Sequencing

  • Sanger vs NGS

  • Whole Genome Sequencing (WGS)

  • Whole Exome Sequencing (WES)

  • RNA-seq

  • Single-cell sequencing

  • Illumina sequencing

  • Flow cell & cluster generation

  • Sequencing by synthesis (SBS)

  • Read depth and coverage

  Session 3: Library Preparation

  • DNA fragmentation

  • Adapter ligation

  • PCR amplification

  • Capture probes

  • Exome enrichment

  Session 4: FASTQ Files & Quality Scores

  • FASTQ structure

  • Read headers

  • Phred scores

  • Sequencing quality

  Practical Session:

  • Linux basics

  • Viewing FASTQ files

  • Sequence lines & quality lines

  • Paired-end reads

  Day 2 — Linux, Alignment and BAM Processing

  Theme: How reads align to the reference genome

  Sessions

  • Linux for Bioinformatics

  • Conda and environment management

  • Alignment concepts

  • BWA MEM and SAM/BAM files

  • Duplicate reads and QC

  • PCR duplicates & optical duplicates

  • CIGAR strings

  Practical Session:

  • Alignment pipeline

  • Duplicate marking

  • BAM inspection

  Day 3 — GATK Best Practices and Variant Calling

  Sessions

  • GATK Best Practices workflow

  • Base Quality Score Recalibration (BQSR)

  • Germline vs Somatic Variant Calling

  • HaplotypeCaller & Mutect2

  • GATK filtering concepts

  • Panel of Normals (PoN)

  • Strand bias & contamination

  • VCF files and normalization

  • bcftools normalization

  Practical Session:

  • Base recalibration

  • PASS variant filtering

  • VCF normalization

  Day 4 — Variant Annotation and ACMG Interpretation

  Theme: How variants gain biological and clinical meaning

  Sessions

  • Variant annotation concepts

  • Annotation databases (dbSNP, ClinVar, COSMIC, gnomAD)

  • ANNOVAR workflow

  • ACMG guidelines and evidence categories

  • Somatic interpretation

  Practical Session:

  • Load ANNOVAR output in R

  • Generate plots

  • Interpret pathogenic variants and VUS burden

  Day 5 — Clinical Interpretation, Pharmacogenomics and Reporting

  Theme: From variants to precision medicine

  Sessions

  • Clinical interpretation of variants

  • Cancer and clinical databases

  • Pharmacogenomics concepts

  • CYP450, TPMT, NUDT15, UGT1A1

  • Stargazer and star alleles

  • Clinical reporting workflows

  • AI in genomics & precision medicine

  Practical Session:

  • Running Stargazer