Module 2 - mestato/EPP622_2026 GitHub Wiki
Module 2 Grading
This module will last for 7 class periods. The grading will be as follows:
- 80% Project-based test
- 20% In class discussion participation (2)
Class 8. Thursday September 10th
- Illumina Slides - Short Read Platforms, Fastq Format, Error Profiles, Intro to lab data
- Lab: Module 2.1 - project set up, conda, fastqc, multiqc
- Homework: Ask an AI assistant of your choice to write you a complete short-read SNP calling pipeline for a haploid fungal genome, starting from paired FASTQ and ending at a filtered VCF. Do not edit it. Do not run it. Submit the raw output verbatim, plus a note recording which model you used, the exact prompt, and the date. Points for doing this are part of your final test.
Class 9. Tuesday September 15th
- Lab: Start on software download so it can run while we talk about read mapping
- Slides: Read mapping and SAM/BAM/CRAM
- Reading
- Nielson 2013 Genotype and SNP calling from next-generation sequencing data - this is for discussion
- Danecek 2021 Twelve years of SAMtools and BCFtools - this is a good reference, not needed for discussion
Class 10. Thursday September 17th
- Discussion: Day 10 discussion seeds
- Lab: Module 2.2 - fastp
Class 11. Tuesday September 22nd
- Slides: File formats (vcf/bcf)
- Lab: Module 2.4 bcftools and vcf filtering
- Optional: Fix conda speed issue (hopefully)
- Homework:
- Download Jbrowse2: https://jbrowse.org/jb2/download/
- Download IGV: https://igv.org/doc/desktop/#DownloadPage/
- Reading for all: Li H 2014. Toward better understanding of artifacts in variant calling from high-coverage sequencing data. - not going to be discussed, but interesting for understanding when and why snp calling fails
- HW Readings: Select the article most relevant to your area of study and be ready to discuss on Thursday with peers who selected the same paper. Each group will report on the most important points to the rest of the class.
- Marees et al., 2018: A tutorial on conducting genome-wide association studies: Quality control and statistical analysis
- Hoban et al., 2016: Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions
- Leache and Oakes, 2017: The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics
- Sun & Li 2026: Advances in haplotype phasing and genotype imputation
- Discussion Seeds:
- What is the key insight you took away from this paper?
- Are there any areas you wish the authors had expanded further that left you with additional questions?
- Was there anything you didn't understand about this paper that we can clarify as a class?
- Share a bit about your own project with your group. Did you learn anything that you can apply to your own work, either technically or conceptually?
Class 12. Thursday September 24th
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Discussion
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Slides: VCF Filtering (Continued)
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Try to find
- Clean SNP - Consistent alt allele, balanced strands, good MAPQ
- Indel-adjacent misalignment - Ragged pileup of "SNPs" beside an indel
- Repeat region - MAPQ 0 reads, spurious calls?
- Strand bias - Alt allele on one strand only
- Homopolymer - Length-variable indel calls
Class 13. Tuesday September 29th
- Slides: https://docs.google.com/presentation/d/10CeNgG8AQG81MJdBoaLDNawafleOTdqpWTqCmpP0FDI/edit?slide=id.p#slide=id.p
- Lab: Module 2.6 SnpEff, SNP Ordination, and Combining VCFs
- Assign test - see below
Class 14. Thursday October 1st
Test 2 help in class
Class 15. Thursday October 8th
Test 2 help in class
Test 2
- Test 2 Explanation & Rubric: Test 2: A celebration of your new SNP calling expertise
- Test 2 Template to Copy into your own GitHub Repo: Test 2 Wiki template raw
- Example of Rendered Test 2 Template: Test 2 Wiki template rendered
- October 13th - Optional deadline to turn in work for Steps 1-6, from fastqc to evaluating your SNP sets against the ground truth set. Zane and I will help you figure out if you have any issues to fix prior to writing the reports.
- October 20th - Final due date