Long reads VCF Preprocessing User Guide8 months ago
Data source | 1. Download phased VCFs for each individual | 2. Merge individual VCFs into a trio VCF | 3. Filter variants for UPDhmm input | 4. UPDhmm analysis in R | Session Info
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UPDhmm User Guide: From Detection to Postprocessing8 months ago
Background | Method overview | Set-up the packages | Loading libraries | Quick start | Detecting and postprocessing UPD events | 1. Load and preprocess the VCFs | 2. Detect UPD events using the HMM-based approach | Results description | 3. Collapse and summarize results per individual | 4. Perform postprocessing analyses | 5. Visualizing UPD events across the genome | Summary | Session Info
VCF Preprocessing User Guide1 years ago
Inputs | 0. Normalize and Left-Align Variants (optional) | 1. Remove Extra Annotations | 2. Merge Trio into a Single VCF | 3. Mask Structural Variant Regions | Session Info