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Getting Started

Work in Progress

This tutorial is under development. Check back soon for a complete walkthrough using example data.

This tutorial will guide you through a complete clam workflow using example data, from raw depth files to population genetic statistics.

What You'll Learn

  • How to prepare input files for clam
  • Generate callable loci with clam loci
  • Calculate π, dxy, and FST with clam stat
  • Interpret and visualize the results

Prerequisites

  • clam installed (see Installation)
  • Basic familiarity with command-line tools
  • Python or R for visualization (optional)

Example Dataset

This tutorial uses simulated data from the clam test suite, representing:

  • 20 samples across 2 populations (Pop1, Pop2)
  • 10 samples per population
  • D4 depth files and a variants-only VCF

Tutorial Outline

Part 1: Prepare Your Data

  • Organize depth files (D4 or GVCF)
  • Create a population file
  • Inspect chromosome names and lengths

Part 2: Generate Callable Loci

  • Choose appropriate depth thresholds
  • Run clam loci with population definitions
  • Examine the output Zarr store

Part 3: Calculate Statistics

  • Run clam stat with the callable loci
  • Understand window-based calculations
  • Explore the output TSV files

Part 4: Analyze Results

  • Load results in Python/R
  • Plot diversity across the genome
  • Compare populations

Coming Soon

Full tutorial content with step-by-step instructions and example code.

In the meantime, see: