Page Index - rsalani13/EPP622-2026-SNPCalling GitHub Wiki
21 page(s) in this GitHub Wiki:
- Home
- AI Analysis ‐ Pipeline Audit
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- Assignment Analysis
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- Directory Structure
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- SNP Calling for EPP622 Exam 2 SET‐UP
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- Step 1: Quality Control (FastQC MultiQC)
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- Step 2: Read Trimming and Filtering (fastp)
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- Step 3: Alignment (bwa‐mem2 samtools)
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- Step 4: Variant Calling (bcftools mpileup call)
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- Step 5: Filtering (bcftools filter)
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- Step 6: Evaluation Against the Truth Set
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