Variant Calling and Structural Genomics Pipeline Design Training Course for Bioinformaticians

Module 1: Foundations of NGS Data, Quality Control, and Read Preprocessing

ü  Overview of Short-Read (Illumina) and Long-Read (PacBio, Oxford Nanopore) Sequencing Technologies

ü  Understanding Genomic File Formats: FASTQ, FASTA, and Quality Score Systems (Phred)

ü  Raw Read Quality Control and Metrics Generation using FastQC and MultiQC

ü  Adapter Trimming, Low-Quality Base Filtering, and Contamination Removal using Trimmomatic and Fastp

ü  Practical Session: Executing quality control workflows on raw paired-end FASTQ data and generating unified MultiQC HTML reports

 

Module 2: High-Accuracy Read Alignment and Post-Alignment Processing

ü  Reference Genome Architecture, Indexing, and Genome Build Comparisons (GRCh38 vs. CHM13 T2T)

ü  Short-Read Alignment Algorithms: Burrows-Wheeler Transform, BWA-MEM, and Bowtie2

ü  Long-Read Alignment Algorithms: Minimap2 and NGMLR

ü  BAM/SAM File Manipulation, Sorting, Indexing, and Coverage Calculation with SAMtools and Sambamba

ü  Marking PCR Duplicates, Base Quality Score Recalibration (BQSR), and Alignment QC with Picard Tools

ü  Practical Session: Aligning raw reads to the human reference genome, sorting BAM files, marking duplicate reads, and computing depth of coverage

 

Module 3: Small Variant Calling Frameworks (SNVs and Indels)

ü  Statistical Foundations of Variant Calling: Bayesian and Maximum Likelihood Models

ü  GATK Best Practices Workflow for Germline Short Variant Discovery (HaplotypeCaller)

ü  Joint Genotyping Strategies for Population-Scale Cohorts (GenotypeGVCFs)

ü  Alternative Variant Callers: FreeBayes and BCFTools Call Pipeline

ü  Hard Filtering vs. Variant Quality Score Recalibration (VQSR) for False-Positive Reduction

ü  Practical Session: Implementing the GATK HaplotypeCaller workflow to identify germline SNVs and indels from aligned BAM files

 

Module 4: Somatic Variant Calling and Cancer Genomics

ü  Distinguishing Somatic Mutations from Germline Variants: Paired Tumor-Normal Analysis Frameworks

ü  Handling Tumor Purity, Subclonal Heterogeneity, and Copy Number Alterations in Cancer

ü  Somatic SNV and Indel Discovery using Mutect2, Strelka2, and VarScan2

ü  Filtering Artifacts using Panel of Normals (PoN) and Population Allele Frequencies

ü  Visualizing Somatic Variants, Mutational Signatures, and Oncogenic Drivers

ü  Practical Session: Running Mutect2 on paired tumor-normal BAM files, building a custom Panel of Normals, and applying artifact filtering

 

Module 5: Structural Variation (SV) Detection in Short-Read Data

ü  Principles of Structural Variation: Deletions, Insertions, Inversions, Duplications, and Translocations

ü  Short-Read SV Detection Signals: Split-Reads, Discordant Read-Pairs, and Read-Depth Alterations

ü  Benchmarking Short-Read SV Callers: Manta, LUMPY, and DELLY

ü  Integrating Ensemble SV Callers for Higher Precision and Sensitivity

ü  Filtering and Genotyping Structural Variants using VCF tools and SURVIVOR

ü  Practical Session: Detecting and genotyping structural variations in short-read data using Manta and evaluating call sets with SURVIVOR

 

Module 6: Long-Read Genomics for Structural Variant Discovery

ü  Advantages of Long-Read Sequencing (PacBio HiFi, Oxford Nanopore) for Complex Genomic Regions

ü  Long-Read Alignment Considerations and Base-Call Error Profiles

ü  Long-Read SV Calling Frameworks: Sniffles2, CuteSV, and PBSV

ü  Characterizing Repetitive Elements, Transposons, and Complex Structural Rearrangements

ü  De Novo Genome Assembly Frameworks for Haplotype-Resolved SV Discovery

ü  Practical Session: Processing Oxford Nanopore and PacBio HiFi data using Minimap2 and Sniffles2 to detect complex structural variants

 

Module 7: Copy Number Variation (CNV) Analysis and Detection

ü  Principles of Copy Number Variation: Germline Copy Number Differences and Somatic Copy Number Alterations

ü  Read-Depth Analysis for CNV Profiling: Normalization Methods and GC-Content Correction

ü  CNV Calling Tools: CNVkit, GATK gCNV, and Control-FREEC

ü  Integrating B-Allele Frequency (BAF) and Log2 Ratios for Allele-Specific CNV Profiling

ü  Visualizing CNV Profiles Across Whole Genomes and Specific Chromosomal Arms

ü  Practical Session: Executing CNVkit on target enrichment/WES data to profile copy number gains and losses and generating diagnostic scatter plots

 

Module 8: Variant Annotation, Filtering, and Functional Effect Prediction

ü  Standardization of Variant Call Format (VCF) and Data Manipulation with BCFTools

ü  Functional Variant Annotation Frameworks: SnpEff, VEP (Variant Effect Predictor), and ANNOVAR

ü  Integrating Population Allele Frequencies (gnomAD, 1000 Genomes) and Pathogenicity Scores (CADD, REVEL)

ü  Prioritizing Rare, Loss-of-Function, and Clinical Variants according to ACMG/AMP Guidelines

ü  Querying and Filtering VCF Files using Slivar, SnpSift, and BCFTools

ü  Practical Session: Annotating a multi-sample VCF using Ensembl VEP, applying custom Slivar filters, and prioritizing pathogenic candidate variants

 

Module 9: Automated Workflow Management with Nextflow and Smakemake

ü  Principles of Declarative and Dataflow Programming for Computational Biology

ü  Building Reproducible Pipelines with Snakemake: Rules, Inputs, Outputs, and Wildcards

ü  Constructing Scalable Workflows with Nextflow: Processes, Channels, and Operators

ü  Managing Pipeline Configuration, Execution Profiles, and Modular Architecture (nf-core)

ü  Handling Error Recovery, Resume Mechanisms, and Dynamic Resource Allocation

ü  Practical Session: Writing a modular Nextflow script to automate read alignment, BAM processing, and variant calling end-to-end

 

Module 10: Containerization, HPC Deployment, and Pipeline Reproducibility

ü  Ensuring Software Reproducibility in Bioinformatics: Bioconda, Docker, and Singularity/Apptainer

ü  Creating Custom Dockerfiles and Singularity Images for Genomic Toolkits

ü  Integrating Containers with Workflow Managers (Nextflow/Snakemake)

ü  Deploying Pipelines on HPC Schedulers (SLURM, PBS) and Cloud Infrastructures (AWS Batch, Google Cloud Life Sciences)

ü  Best Practices for Open-Science Code Documentation, Version Control with Git, and GitHub Deployment

ü  Practical Session: Containerizing a variant calling pipeline with Singularity and deploying it on a SLURM-managed HPC cluster using Nextflow

About Our Trainers

 

Our trainers are senior bioinformaticians, computational genomicists, and software engineers with over 15 years of practical experience in high-throughput sequencing data analysis, pipeline engineering, and academic/industrial R&D. They have led large-scale genomic projects across clinical diagnostics, cancer research, agricultural biotechnology, and evolutionary genomics. Having authored numerous peer-reviewed publications in high-impact scientific journals and contributed to open-source bioinformatics tools, our instruction team brings unmatched technical depth and practical insights directly into the classroom.

 

Quality Statement

 

Phoenix Center for Policy, Research and Training is committed to delivering world-class, practical, and impact-driven professional development programs. We adhere to rigorous instructional standards, continuously updating our curriculum to reflect the latest advancements in next-generation sequencing, long-read technologies, and computational frameworks. Our hands-on training environments, expert mentorship, and industry-aligned evaluation metrics ensure that every participant achieves actionable competency and immediate operational capability upon course completion.

 

Tailor-Made Courses

 

We understand that every organization has unique challenges and opportunities as well as unique training needs. Phoenix Training Center offers tailor-made courses designed to address specific requirements and challenges faced by your team or organization. Whether you need a customized curriculum, a specific duration, or on-site delivery, we can adapt our expertise to provide a training solution that perfectly aligns with your objectives. We can customize this Course to focus on your industry, specific risk profile, or internal stakeholder dynamics. Contact us to discuss how we can create a bespoke training program that maximizes value and impact for your team. For further inquiries, please contact us on Tel: +254720272325 / +254737296202 or Email: training@phoenixtrainingcenter.com.

 

Admission Criteria

 

ü  Participants should be reasonably proficient in English.

ü  Applicants must live up to Phoenix Center for Policy, Research and Training admission criteria.

 

Terms and Conditions

 

ü  Discounts: Organizations sponsoring Four Participants will have the 5th attend Free

ü  What is catered for by the Course Fees: Fees cater for all requirements for the training – Learning materials, Lunches, Teas, Snacks and Certification. All participants will additionally cater for their travel and accommodation expenses, visa application, insurance, and other personal expenses.

ü  Certificate Awarded: Participants are awarded Certificates of Participation at the end of the training.

ü  Course Improvement: The program content shown here is for guidance purposes only. Our continuous course improvement process may lead to changes in topics and course structure.

ü  Approval of Course: Our Programs are NITA Approved. Participating organizations can therefore claim reimbursement on fees paid in accordance with NITA Rules.

 

Booking for Training

 

Kindly send an email to the Training Officer on training@phoenixtrainingcenter.com and we will send you a registration form. We advise you to book early to avoid missing a seat to this training. Or call us on +254720272325 / +254737296202

 

Payment Options

 

We provide 3 payment options, choose one for your convenience, and kindly make payments a week before the training starts (at least 5 to 7 days before the Training start date) to reserve your seat:

ü  Groups of 5 People and Above – Cheque Payments to: Phoenix Center for Policy, Research and Training Limited should be paid in advance, a week before the training starts.

ü  Invoice: We can send a bill directly to you or your company.

ü  Deposit directly into Bank Account (Account details provided upon request)

 

Cancellation Policy

 

ü  Payment for all courses includes a registration fee, which is non-refundable, and equals 15% of the total sum of the course fee.

ü  Participants may cancel attendance 14 days or more prior to the training commencement date.

ü  No refunds will be made 14 days or less before the training commencement date. However, participants who are unable to attend may opt to attend a similar training course at a later date or send a substitute participant provided the participation criteria have been met.

 

Accommodation and Airport Pick-up

 

For physical training attendees, we can assist with recommendations for accommodation near the training venue. Airport pick-up services can also be arranged upon request to ensure a smooth arrival. Please inform us of your travel details in advance if you require these services. For reservations contact the Training Officer on Email: training@phoenixtrainingcenter.com or on Tel: +254720272325 / +254737296202.