Home - AreliDGS/EPP622-2026-SNPCalling GitHub Wiki
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