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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  • Tutorial
  • Congratulations!

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  1. Week 8
  2. NGS

Variant Calling With GATK

This page takes an estimated 45 minutes to complete.

PreviousNGSNextPractice 1

Last updated 3 years ago

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Variant calling entails identifying single nucleotide polymorphisms (SNPs) and small insertions and deletion (indels) from NGS data.

Help Material

For this page, you will use the and the presentation below as help material.

Tutorial

  1. Copy variant_calling_files.tar.gz archive from /home/shared/ngs_data/variant_calling folder to your home directory and extract files from the archive.

  2. Read the tutorial run the commands from the variant_calling_script.sh file according to the steps in the tutorial (commands presented in this tutorial will not work in your server as the software and input data are different)

  3. After successfully running all commands from the variant_calling_script.sh file you should get filtered .vcf files for SNPs and Indels. For visualization of calculated results download these files to your computer:

    • dedup_reads.bam

    • dedup_reads.bam.bai

    • filtered_snps.vcf

    • filtered_snps.vcf.idx

    • ecoli_rel606.fasta

  4. Open IGV browser in your computer and load downloaded ecoli_rel606.fasta genome via Genomes > “Load Genom from file…”.

  5. Now you can load bam and .vcf files via File > “Load from file…”. You can check mutations and navigate through the genome by inserting coordinates on top of the window (example coordinate: CP000819.1:2,446,706-2,447,373)

Congratulations!

If you made it here, then congratulations! You have successfully completed this section. Move to the next portion of the guide with the arrow buttons below.

In the step, please skip the “Setting up your environment..” parts and start from “1) Alignment”, as we already have a ready environment in our server. Please also skip the “6) Base Quality Score Recalibration” section.

In the section skip the “3) Annotation” part. For the visualization of the results in the IGV (Integrative genomic viewer) browser, you should and install IGV on your computer.

Pre-Processing
Variant discovery
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Variant Calling with GATK website