Home

EPP622-2026 / Test 2: Professional SNP Calling Pipeline

This project implements a pipeline to identify and evaluate 5,000 engineered SNPs in the Saccharomyces cerevisiae genome.

---

• Student Name: Areli Daniela Gonzalez Sandoval
• Compute Server: Linux cluster, UTK property.
• Repository URL: EPP622-2026-SNPCalling

---

Laboratory Test Index

The pipeline documentation is divided into independent modules, use the links below to navigate through each analysis phase:

Initial phase and workspace setup

• 0. Environment setup and data preparation
  • Directory infrastructure, symbolic links to raw datasets, and environment verification.

Quality control and read preprocessing

• 1. Initial quality control (FastQC + MultiQC)
  • Analysis of raw samples A, B, C, and D.
• 2. Read trimming and filtering (fastp)
  • Adapter removal and manual overriding of the poly-G tail clipping mechanism.

Alignment and variant calling

• 3. Alignment to reference genome (bwa-mem2)
  • Mapping reads against the s. cerevisiae reference and metrics extraction via samtools.
• 4. Raw variant calling (bcftools)
  • Genotyping and initial identification of raw SNPs and indels using mpileup.
• 5. Stringent variant filtering (bcftools filter)
  • Comparative analysis between gentle and stringent filtration thresholds.

Validation and critical assessment

• 6. Evaluation against the truth set
  • *Performance benchmarking metrics (precision, recall, F1-score), verification of false positives/negatives via JBrowse 2

Human vs IA

Reflexion of learning bioinformatics and the impact of AI in education

---

Paths for instructor review

The following path locations target the report files:

• Pre-trimming MultiQC report: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/01_multiqc_raw_report.html
• Post-trimming MultiQC report: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/02_multiqc_trimmed_report.html
• BWA-MEM2 alignment MultiQC report: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/03_multiqc_alignment_report.html
• BCFtools stats - RAW SNP set: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/04_variant_calling/yeast_data.raw.stats.txt
• BCFtools stats - GENTLE filtered set: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/05_filtering/yeast_data.gentle.stats.txt
• BCFtools stats - STRINGENT filtered set: /lustre/isaac24/proj/UTK0505/agonza84/EPP622-2026-SNPCalling/results/05_filtering/yeast_data.stringent.stats.txt