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  • Clindet documentation

Contents:

  • Quick Start
    • 1. Clindet
    • 2. Setup Clindet
    • 3. Use case
  • DNAseq analysis
    • 1. Whole exome sequence data analysis
      • 1.1. ClinDet WXS workflow
    • 2. Whole genome sequence data analysis
      • 2.1. ClinDet WGS workflow
  • RNAseq analysis
    • 1. ClinDet RNA-seq workflow
  • Use Case
    • 1. Use case I: SNV and CNV calling from Whole exome sequencing data
    • 2. Use case II: Fusion genes detection from multiple myeloma patient RNA-seq
    • 3. Use case III: Whole genome sequencing of COLO829 cell line
    • 4. Use case IV: Quantifying​​ the contributions of DNA repair defective gene mutations to mutational signatures(C.elegans)
    • 5. Use case V: Switching to different genome version (e.g. hg38)
  • A Gym for Clinical NGS Data Analysis Workflows
    • 1. Clinical Omics Benchmark Datasets
    • 2. Benchmark
  • snakemake/clindet: Citations
  • .rst

Whole genome sequence data analysis

2. Whole genome sequence data analysis#

  • 2.1. ClinDet WGS workflow
    • 2.1.1. QC and preprocess
    • 2.1.2. Small variants (SNVs/Indels)
    • 2.1.3. Structural variants
    • 2.1.4. Copy Number Variants
    • 2.1.5. MultiQC
    • 2.1.6. Case Reports
    • 2.1.7. Implementation

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1.1. ClinDet WXS workflow

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2.1. ClinDet WGS workflow

By Yuliang Zhang

© Copyright 2024, Yuliang Zhang.