Primary contributor: Maria Nikoghosyan
Contributing authors: Nate Zadirako, Mariia Arakelyan
| Date (2025) | Time | Topic | Folder |
|---|---|---|---|
| 13 August | 11:00 – 12:00 | Lecture: Genomic Variations | Genetic variations/ |
| 13 August | 12:00 – 13:00 | Practice: Variant Calling | varinat_calling/ |
| 13 August | 14:00 – 15:00 | Practice: VCF File Manipulation | vcf_file_manipulation/ |
| 14 August | 11:00 – 12:00 | Lecture: Integrative Genomics Viewer (IGV) | Integrative_Genomics_Viewer_(IGV)/ |
| 14 August | 12:00 – 13:00 | Practice: Integrative Genomics Viewer (IGV) | Integrative_Genomics_Viewer_(IGV)/ |
Genomic variations are the differences in DNA sequence—such as single-nucleotide polymorphisms (SNPs), insertions, deletions, and structural rearrangements—that distinguish individuals or populations and underlie traits, evolution, and disease. Variant calling is the computational process of comparing high-throughput sequencing reads to a reference genome to detect and catalog these variations with quality metrics. Accurate variant calling transforms raw sequencing data into actionable biological insights for research and clinical applications.
Here you will find the slides on genomic variation and variant calling
Here you will find the slides on how to visualize NGS data using the Integrative Genomics Viewer (IGV).
In the variant_calling folder, you will find the materials for the practical session on variant calling.
- variant_calling_pipeline.md — a step-by-step guide to the variant-calling pipeline. All file paths are specified for their locations on the server where you will execute the commands.
In the vcf_file_manipulation folder, you will find the materials for the practical session related to VCF file manipulations.
Adjust paths
Prepare VCF manipulation practice [Maria A]
Prepare IGV presentation and practice [Maria A & Maria N]