Overview | Features | Requirements | Installation | From GitHub (recommended — latest version) | From release tarball | CLI Setup | Verify installation | Quick Start Examples | 1. Basic imputation | 2. Imputation with missing SNP fill-in | 3. Training a new model | 4. Evaluating a trained model | Core Usage Reference | Help | impute command | Required flags | Optional flags | train command | KIR file format | evaluate command | Pre-phasing the KIR Region | hg19 | hg38 | Improving Imputation Accuracy | Option A: Local pre-imputation (built-in, quick) | Option B: External pre-imputation (recommended for highest accuracy) | Option C: Force imputation (not recommended) | Next Steps

Overview | Prerequisites | Step 1: Prepare Input Data | Step 2: Run Basic PONG2 Imputation | Step 3: Check SNP Overlap | Step 4: Pre-imputation (when SNP overlap < 50%) | Pre-phase with Eagle2 | hg19 | hg38 | Option A: Local Pre-imputation with minimac4 (built-in) | Option B: External Pre-imputation (recommended for highest accuracy) | Step B1: Export phased VCF | Step B2: Upload to Michigan Imputation Server | Step B3: Download and convert imputed VCF to PLINK | Step B4: Run PONG2 on imputed data | Option C: Force imputation (not recommended) | Step 5: Interpreting Output | Output CSV format | Large sample datasets | Summary: Which Workflow to Choose? | Next Steps

Overview | 1. Installation and Setup | 2. Example Data | 3. KIR Genotype Prediction | 4. Model Training | 5. Model Evaluation | 6. CLI Usage | Session Info

Overview | Prerequisites | Step 1: Prepare Input Data | 1a. Reference genotypes (--bfile) | Using the 1000 Genomes Project (1KGP) as reference panel | Using your own reference dataset | 1b. Known KIR allele calls (--kfile) | Format | Rules | Step 2: Run Training | With optional parameters | Key training parameters | Step 3: Training Output | Step 4: Evaluate Model Performance | Option A: Evaluate from the terminal (recommended) | Option B: Evaluate in R | Step 5: Use a Custom Model for Imputation | Troubleshooting | Next Steps

Overview | Features | Requirements | Installation | From GitHub (recommended — latest version) | From release tarball | CLI Setup | Verify installation | Quick Start Examples | 1. Basic imputation | 2. Imputation with missing SNP fill-in | 3. Training a new model | 4. Evaluating a trained model | Core Usage Reference | Help | impute command | Required flags | Optional flags | train command | KIR file format | evaluate command | Pre-phasing the KIR Region | hg19 | hg38 | Improving Imputation Accuracy | Option A: Local pre-imputation (built-in, quick) | Option B: External pre-imputation (recommended for highest accuracy) | Option C: Force imputation (not recommended) | Next Steps

Overview | Prerequisites | Step 1: Prepare Input Data | Step 2: Run Basic PONG2 Imputation | Step 3: Check SNP Overlap | Step 4: Pre-imputation (when SNP overlap < 50%) | Pre-phase with Eagle2 | hg19 | hg38 | Option A: Local Pre-imputation with minimac4 (built-in) | Option B: External Pre-imputation (recommended for highest accuracy) | Step B1: Export phased VCF | Step B2: Upload to Michigan Imputation Server | Step B3: Download and convert imputed VCF to PLINK | Step B4: Run PONG2 on imputed data | Option C: Force imputation (not recommended) | Step 5: Interpreting Output | Output CSV format | Large sample datasets | Summary: Which Workflow to Choose? | Next Steps

Overview | 1. Installation and Setup | 2. Example Data | 3. KIR Genotype Prediction | 4. Model Training | 5. Model Evaluation | 6. CLI Usage | Session Info

Overview | Prerequisites | Step 1: Prepare Input Data | 1a. Reference genotypes (--bfile) | Using the 1000 Genomes Project (1KGP) as reference panel | Using your own reference dataset | 1b. Known KIR allele calls (--kfile) | Format | Rules | Step 2: Run Training | With optional parameters | Key training parameters | Step 3: Training Output | Step 4: Evaluate Model Performance | Option A: Evaluate from the terminal (recommended) | Option B: Evaluate in R | Step 5: Use a Custom Model for Imputation | Troubleshooting | Next Steps