Please register to attend this workshop at the bottom of this page. After filling out the registration form, we will email you the Zoom link.

Amarel account: You need an Amarel account to participate in the lab section Apply here as soon as possible.

VPN setup: You have to be connected on Rutgers’ network or be on VPN to access Amarel resources.

If you have questions or need help, please contact Janet Chang.

1. Introduction – The Basics of Variant Analysis

• Concepts of genetic variant
• The journey of variant study
• Significance
• Challenges

2. Variant Analysis –Overview

• Workflow and informatics tools
• Variant detection methods
• Variant calling algorithms
• Variant annotation and functional prediction
• Variant prioritization, filtering, and validation

3. Variant Analysis – Getting ready

• File format—fastq, vcf, bed, bam/sam
• Variant ID and databases
• Variant Reporting
• Variant visualization
• ** Variant analysis of COVID-19 genomes

4. Variant calling pipeline example — GATK

• GATK Best practices
• Pre-processing
  • BWA, picard and GATK-format, Dealing with duplicates,
    Base recalibration (BQSR)
• Variant discovery
  • HaplotypeCaller, Germline and somatic mutation calling,
    Variant recalibration (VQSR), Variant Filtering
• Preliminary analysis
  • Variant annotation/function prediction
    Variant evaluation

5. Variant calling pipeline example — Varscan2, Samtools

• SNP/INDEL calling using Varscan2
• SNP/INDEL calling using samtools/bcftools
• Filtering and function prediction

6. Labs

• Lab1 — Pre-processing, QC, mapping, and reference preparation
• Lab2 — GATK pipeline
• Lab3 — Samtools and varscan2 pipelines
• Lab4 — Variant annotation/ Functional prediction
• Lab5 — Visualization
• Lab6 — Manage your jobs using slurm job scheduler