BIO326_2026

# Structural Variant Teaching Dataset Bos taurus – Chromosome 13 (IGV-ready subset)---## OverviewThis 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 lociThe 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 PurposeThis 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.---