Introduction to genome variation analysis using NGS

Prerequisites

This course provides an introduction to the analysis of human genome sequence variation with next generation sequencing data (NGS), including:

• an introduction to genetic variation as well as data formats and analysis workflows commonly used in NGS data analysis;
• an overview of available analytical tools and discussion of their limitations; and
• hands-on experience with common computational workflows for analysing genome sequence variation using bioinformatics and computational genomics approaches.

A draft agenda can be found here

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Further details regarding eligibility criteria are available here

• Basic experience of command line UNIX
• Sufficient UNIX experience might be obtained from one of the many UNIX tutorials available online.

Number of sessions: 2

After this course you should be able to:

• Recognize the challenges and pitfalls of the analysis of human genome sequence variation
• Recognize issues with the data
• Visualize alignments and variants using a genome viewer
• Evaluate the quality of your alignments and your variants
• Understand the standard file formats for representing variant data
• Apply filters to your list of variants
• Functionally annotate variants

During this course you will learn about:

• Introduction to genome variation
• Experimental design
• Genome sequence alignment
• Data quality assessment
• Variant calling
• Variant filtering, effect prediction and prioritisation
• Genome-wide association

Presentations, demonstrations and practicals

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

2

A number of times per year

• Variant Analysis with GATK