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rsalani13
EPP622-2026-SNPCalling

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rsalani13 edited this page Oct 1, 2026 · 1 revision

Welcome to the EPP622-2026-SNPCalling wiki!

Wiki pages Pages 11

Home
AI Analysis ‐ Pipeline Audit
Assignment Analysis
Directory Structure
SNP Calling for EPP622 Exam 2 SET‐UP
Step 1: Quality Control (FastQC MultiQC)
Step 2: Read Trimming and Filtering (fastp)
Step 3: Alignment (bwa‐mem2 samtools)
Step 4: Variant Calling (bcftools mpileup call)
Step 5: Filtering (bcftools filter)
Step 6: Evaluation Against the Truth Set

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