BIO326_2026

# Structural Variant Teaching Dataset Bos taurus – Chromosome 13 (IGV-ready subset) --- ## Overview This dataset was prepared for teaching structural variant (SV) analysis using long-read sequencing data (Oxford Nanopore). The material includes: - Two samples (2024 and 2025)- High-confidence structural variants- Chromosome 13 only- Reads restricted to ±20 kb around selected SV loci The dataset is intentionally reduced in size so that it loads quickly in IGV and can be used in classroom settings without heavy computational requirements. --- ## Dataset Contents ### Reference Genome (Chromosome 13 only) - `Bos_taurus_chr13.fa`- `Bos_taurus_chr13.fa.fai` Reference sequence used for alignment and visualization. --- ### Alignment Files - `2024_chr13_teaching_20kb.bam`- `2024_chr13_teaching_20kb.bam.bai`- `2025_chr13_teaching_20kb.bam`- `2025_chr13_teaching_20kb.bam.bai` These BAM files contain only reads overlapping selected structural variant regions (±20 kb). They allow direct comparison between two samples. --- ### Structural Variant Calls - `joint_chr13_teaching_20kb.vcf.gz`- `joint_chr13_teaching_20kb.vcf.gz.tbi` Joint multi-sample SV calls generated using Sniffles2 (v2.0.7). High-confidence variants were selected using the following criteria: - PRECISE calls only- QUAL ≥ 50- One sample homozygous alternate (1/1)- The other sample homozygous reference (0/0)- Variant read support ≥ 4- No conflicting reference reads in the alternate sample --- ### Gene Annotation - `Bos_taurus_chr13.gtf.gz`- `Bos_taurus_chr13.gtf.gz.tbi` Ensembl gene annotation restricted to chromosome 13. --- ## How to Use in IGV1. Load the reference genome (`Bos_taurus_chr13.fa`)2. Load both BAM files3. Load the VCF file4. Load the gene annotation (GTF)5. Navigate to a variant coordinate6. Compare genotype and read support between samples --- ## Educational Purpose This dataset enables students to: - Visualize insertions and deletions in long-read alignments- Compare genotypes between two samples- Interpret read-level support (DV / DR)- Understand how structural variants are represented in VCF- Connect structural variation to gene structure- Investigate gene function using public databases --- ## Software Required - IGV (recommended for visualization)- samtools- bcftools- bedtools- Sniffles2 (for reproducibility) --- ## Notes - Data were derived from course-based research activities.- Only chromosome 13 is included.- Only selected high-confidence SV regions are retained.- The dataset is intended for teaching and demonstration purposes. ---