---
name: "variant-analysis"
type: "use"
topic_type: technology
title: "Variant Analysis"
summary: |
    Genetic differences (variants) between healthy and diseased tissue,
    between individuals of a population, or between strains of an organism
    can provide mechanistic insight into disease processes and the natural
    function of affected genes.

    The tutorials in this section show how to detect evidence for
    genetic variants in next-generation sequencing data, a process termed
    variant calling.

    Of equal importance, they also demonstrate how you can interpret, for
    a range of different organisms, the resulting sets of variants by
    predicting their molecular effects on genes and proteins, by
    annotating previously observed variants with published knowledge, and
    by trying to link phenotypes of the sequenced samples to their variant
    genotypes.
docker_image: "quay.io/galaxy/variant-analysis-training"
edam_ontology: ["topic_0199"]
requirements:
  -
    type: "internal"
    topic_name: introduction
  -
    type: "internal"
    topic_name: sequence-analysis
    tutorials:
      - quality-control
      - mapping

editorial_board:
  - bebatut
  - wm75
  - bgruening
  - nekrut
  - tflowers15

subtopics:
  - id: introduction
    title: "Introduction"
    description: "Concepts of variant and genotype calling"
  - id: model-organisms
    title: "Model Organisms"
    description: "Variant calling for studying genomics of model organisms"
  - id: one-health
    title: "One Health"
    description: "Variant calling for monitoring and preventing health threats"
  - id: human-genetics-cancer
    title: "Human Genetics and Cancer"
    description: "Variant calling pipelines for studying human genetic diseases and cancer"
  - id: data-management
    title: "Data Management"
    description: "Variant calling pipelines for interacting with human genetic databases"

references:
  -
    authors: "Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan"
    title: "GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations"
    link: "http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003153"
    summary: "GEMINI query is the most versatile of all the GEMINI tools. You can use it to ask questions in simple SQL"
  -
    authors: "Rasmus Nielsen, Joshua S. Paul, Anders Albrechtsen & Yun S. Song"
    title: "Genotype and SNP calling from next-generation sequencing data"
    link: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/"
    summary: "Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes."
  -
    authors: "Erik Garrison and Gabor Marth"
    title: "Haplotype-based variant detection from short-read sequencing"
    link: "https://www.researchgate.net/publication/229157122_Haplotype-based_variant_detection_from_short-read_sequencing"
    summary: "The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods, such as Bayesian statistical framework."
  -
    authors: "Aaron R. Quinlan"
    title: "Introduction to GEMINI"
    link: "https://s3.amazonaws.com/gemini-tutorials/Intro-To-Gemini.pdf"
    summary: "GEMINI query is the most versatile of all the GEMINI tools. You can use it to ask questions in simple SQL"
  -
    authors: "Torsten Seemann"
    title: "Snippy: Rapid bacterial SNP calling and core genome alignments"
    link: "https://github.com/tseemann/snippy"
    summary: "Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels)."
  -
    authors: "Wolfgang Maier"
    title: "MiModD Documentation"
    link: "http://mimodd.readthedocs.io/en/latest/"
    summary: "MiModD is a comprehensive software package for mapping-by-sequencing analyses"
  -
    authors: "Korbinian Schneeberger"
    title: "Using next-generation sequencing to isolate mutant genes from forward genetic screens"
    link: "https://www.researchgate.net/profile/Korbinian_Schneeberger/publication/264904703_Using_next-generation_sequencing_to_isolate_mutant_genes_from_forward_genetic_screens/"
    summary: "Mapping the location of causal mutations using genetic crosses has traditionally been a complex procedure, but next-generation sequencing now allows the rapid identification of causal mutations even in complex genetic backgrounds"