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GRiD 0.1 documentation
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GRiD 0.1 documentation

Getting Started

  • Welcome to GRiD’s documentation!
  • Getting Started
  • Computing IBS/IBD Neighbors

Examples

  • Example Pipeline Jobs
    • 1000 Genomes Full Pipeline Example
    • IBS/IBD Neighbor Computation Example

Algorithms

  • Algorithms
    • Read Counting
    • Coverage Estimation
    • Coverage Normalization
    • Nearest-Neighbor Identification
    • Diploid Copy Number Estimation
    • Haplotype Inference

Project

  • Contributing
  • Code of Conduct

Paper

  • Paper

API Reference

  • API Reference
    • Core
    • Read Counting
    • Coverage Estimation
    • Coverage Normalization
    • Nearest-Neighbor Identification
    • Diploid Copy Number Estimation
    • Haplotype Inference
    • CRAM Index Management
    • Utilities & Helper Functions
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Example Pipeline Jobs¶

The GRiD documentation provides examples for running the full pipeline on an HPC cluster and for computing the IBS/IBD neighbors required by Step 5 (haplotype inference).

Examples

  • 1000 Genomes Full Pipeline Example
  • IBS/IBD Neighbor Computation Example
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1000 Genomes Full Pipeline Example
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Computing IBS/IBD Neighbors
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