Statistical Genetics and Genomics

  1. Next-Generation Sequencing in Genetics
    1. Sequencing Technologies
      1. Whole Genome Sequencing
        1. Library Preparation
          1. Sequencing Platforms
            1. Coverage Considerations
              1. Cost-Benefit Analysis
              2. Whole Exome Sequencing
                1. Target Capture Methods
                  1. Exome Design
                    1. Coverage Uniformity
                      1. Limitations and Biases
                      2. Targeted Sequencing
                        1. Panel Design
                          1. Amplicon Sequencing
                            1. Hybrid Capture
                            2. RNA Sequencing
                              1. Library Preparation Methods
                                1. Strand-Specific Protocols
                                  1. Single-Cell RNA-Seq
                                2. Data Processing Pipeline
                                  1. Raw Data Quality Assessment
                                    1. FASTQ Format
                                      1. Quality Scores
                                        1. Adapter Contamination
                                          1. Base Quality Distributions
                                          2. Read Alignment
                                            1. Reference Genome Selection
                                              1. Alignment Algorithms
                                                1. BWA and Bowtie
                                                  1. STAR for RNA-Seq
                                                  2. Post-Alignment Processing
                                                    1. Duplicate Removal
                                                      1. Base Quality Recalibration
                                                        1. Indel Realignment
                                                          1. Quality Metrics
                                                        2. Variant Calling
                                                          1. SNP and Indel Detection
                                                            1. GATK Best Practices
                                                              1. FreeBayes
                                                                1. SAMtools
                                                                  1. Variant Quality Metrics
                                                                  2. Structural Variant Calling
                                                                    1. Read-Pair Methods
                                                                      1. Split-Read Methods
                                                                        1. Read-Depth Methods
                                                                          1. Assembly-Based Methods
                                                                          2. Copy Number Variation Detection
                                                                            1. Read-Depth Analysis
                                                                              1. Hidden Markov Models
                                                                                1. Segmentation Algorithms
                                                                              2. Variant Filtering and Annotation
                                                                                1. Quality-Based Filtering
                                                                                  1. Depth Filters
                                                                                    1. Quality Score Filters
                                                                                      1. Strand Bias Filters
                                                                                      2. Population-Based Filtering
                                                                                        1. Allele Frequency Filters
                                                                                          1. Hardy-Weinberg Filters
                                                                                          2. Functional Annotation
                                                                                            1. Variant Effect Predictor
                                                                                              1. ANNOVAR
                                                                                                1. SnpEff
                                                                                                  1. Custom Annotation Pipelines
                                                                                                2. Rare Variant Association Analysis
                                                                                                  1. Challenges in Rare Variant Analysis
                                                                                                    1. Power Limitations
                                                                                                      1. Population Stratification
                                                                                                        1. Technical Artifacts
                                                                                                        2. Burden Tests
                                                                                                          1. Simple Burden Tests
                                                                                                            1. Weighted Burden Tests
                                                                                                              1. Variable Threshold Tests
                                                                                                              2. Variance Component Tests
                                                                                                                1. SKAT Method
                                                                                                                  1. SKAT-O
                                                                                                                    1. Kernel-Based Approaches
                                                                                                                    2. Combined Tests
                                                                                                                      1. SKAT-O Optimal Test
                                                                                                                        1. Meta-Analysis Methods
                                                                                                                          1. Conditional Analysis

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                                                                                                                      9. Advanced Statistical Methods