GRiD — Genomic Repeat inference from Depth

A Python pipeline for haplotype-resolved VNTR copy number estimation from short-read whole-genome sequencing data. Developed for and validated on the KIV-2 VNTR in the LPA gene; the core depth-normalization framework is applicable to any large VNTR locus.

Getting Started

• Welcome to GRiD’s documentation!
  • GRiD — Genomic Repeat inference from Depth
• Getting Started
  • Global Settings
  • Step 1 — index
  • Step 2 — count_reads
  • Step 3 — mosdepth
  • Step 4 — compute_diploid_genotypes
  • Step 5 — compute_haploid_genotypes
  • Full Example Config
• Computing IBS/IBD Neighbors
  • Dependencies
  • Compilation
  • Required Input Files
  • Running the Program
  • Output Format
  • Passing the Output to GRiD

Examples

• Example Pipeline Jobs

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
  • Command-Line Interface
  • Core
  • Pipeline Steps
  • Utilities