Page Index - AreliDGS/EPP622-2026-SNPCalling GitHub Wiki

25 page(s) in this GitHub Wiki:

• Home
• EPP622-2026 / Test 2: Professional SNP Calling Pipeline
• Laboratory Test Index
• Initial phase and workspace setup
• Quality control and read preprocessing
• Alignment and variant calling
• Validation and critical assessment
• Human vs IA
• Paths for instructor review
• 0. Environment Setup and Data Preparation
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• 1. Initial Quality Control (FastQC MultiQC)
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• 2. Read Trimming and Filtering (fastp)
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• 3. Alignment to Reference Genome (bwa‐mem2)
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• 4. Raw Variant Calling (bcftools)
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• 5. Filtering (bcftools ‐ two scenarios)
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• 6. Evaluation Against the Truth Set
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• Humans vs IA
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