Population Genomics in Practice 2025
  • Slides
  • Exercises
  • Code recipes
  1. Slides
  2. Variant calling
  3. Listing
  • Slides
    • Listing
    • Introduction
      • Population genomics in practice
    • Population genetics foundations
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      • Data and definitions
      • Alleles and genealogies
      • Linkage disequilibrium
      • The Wright-Fisher model
      • Genetic diversity
      • Selection
    • Variant calling
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      • DNA sequencing data
      • Read mapping
      • Variant calling and genotyping
      • Variant calling workflows
    • Variant filtering
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      • Variant filtering
      • Depth filtering
    • Genetic diversity
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      • Genetic diversity
    • Population structure
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      • Principal component analysis
      • Admixture
    • Demography
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    • Selection
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    • Simulation
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      • Brief introduction to simulation packages and stdpopsim
      • Primer on the coalescent and forward simulation
      • Ancestral recombination graph inference
  • Exercises
    • Listing
    • Data
      • Compute environment
      • Monkeyflowers dataset
    • Variant calling
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      • Variant calling introduction
      • Data quality control
      • Read mapping and duplicate removal
      • Variant calling workflow
    • Variant filtering
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      • Basic variant filtering
      • Depth filtering on invariant sites
    • Recombination and linkage
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      • Linkage disequilibrium decay
    • Genetic diversity
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      • Genetic diversity landscapes
    • Population structure
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      • Principal component analysis
      • Admixture
      • D-statistics
    • Simulation
      • Listing
      • HOWTO
      • Introduction to stdpopsim
      • Simulating selection with stdpopsim
      • Introduction to simulation with msprime
  • Code recipes
    • Code recipes

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Variant calling

Collection of presentations on DNA sequencing and variant calling.
Author

Per Unneberg

Published

18-Sep-2025

About

Collection of presentations on DNA sequencing and variant calling.

Listing

Title Description
DNA sequencing data
Read mapping
Variant calling and genotyping
Variant calling workflows Introduction to variant calling and genotyping using workflow managers.
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2025 NBIS | GPL-3 License

 

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