ABI OMICSS Guide 2021
  • Welcome
  • Week 1
    • Molecular Biology
      • Introduction to Biology
      • Macromolecules
      • DNA & RNA
      • Cell Division
    • Command-Line
      • Connecting to the Server
      • The Linux Command-Line For Beginners
      • The Bash Terminal
    • R Programming
      • Getting Started
      • The Basics
      • Data Types
    • Week 1 Exam
  • Week 2
    • Molecular Biology
      • DNA Proofreading And Repair
      • Telomeres and Telomerase
      • Genes
      • The One Gene, One Enzyme Hypothesis
      • Transcription
      • Translation
    • R Programming
      • Data Types (continuation)
      • Reading Data
      • Subsetting
      • Control Structures
      • Functions
      • Scoping Rules
    • Week 2 Exam
  • Week 3
    • Molecular Biology
      • tRNA and Ribosomes
      • Stages of Translation & Protein Targeting
      • Heredity
      • Probabilities In Genetics
    • R Programming
      • Loop Functions
      • Base Graphics
    • Statistics and R
      • The Basics
    • Week 3 Exam
  • Week 4
    • Molecular Biology
      • Interesting Cases of Genes
      • The Chromosomal Basis of Inheritance
      • Variation in Species
      • Phenotype plasticity
    • R Programming
      • Practice 2
      • Practice 3
    • Statistics and R
      • Random Variables and Probability Distributions
      • Central Limit Theorem
    • Week 4 Exam
  • Week 5
    • Statistics and R
      • Confidence Interval
      • Introduction to Inference
      • t-distribution and Comparing Means
      • Linear Models
    • Experimental Techniques
      • Polymerase Chain Reaction (PCR)
      • Gel Electrophoresis
      • Sanger Sequencing
      • NGS Sequencing
    • Week 5 Exam
  • Week 6
    • Statistics and R
      • Power
      • ANOVA
      • Covariance and Correlation
    • NGS
      • Basic Unix Commands
      • Sequences and Genomic Features
      • FastQC
      • Practice Exercises
    • Week 6 Exam
  • Week 7
    • Statistics and R
      • Monte Carlo Simulation
      • Exploratory Data Analysis
      • Linear Regression
    • NGS
      • BEDtools
      • Alignment and Sequence Variation
      • Integrated Genomics Viewer
    • Week 7 Exam
  • Week 8
    • NGS
      • Variant Calling With GATK
      • Practice 1
    • Week 8 Exam
  • Module Syllabi
  • Additional Resources
  • Conclusion
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  1. Week 7
  2. NGS

Alignment and Sequence Variation

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Last updated 3 years ago

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The bioinformatics workflow for handling and for detecting sequence variations starts with the alignment of reads to the genome, followed by what we call variant calling.

To learn more about this topic, watch the following videos from , and return here afterward:

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the Coursera course
Alignment and Sequence Variation 1: Overview
Alignment and Sequence Variation 2: Alignment and Variant Detection Tools
Alignment and Sequence Variation 3: VCF
Alignment and Sequence Variation 4: Bowie
Alignment and Sequence Variation 5: BWA