Variant calling

All data and files for this section can be found in the EBI training FTP.

Introduction to Variant calling: SNPs and Indels

Trainers: Raheleh Rahbari and Rashesh Sanghvi

Overview: This lecture covers detection of genome variants such as SNPs and indels, via variant calling.

Learning outcomes:

By the end of this session you will be able to:

• Define variant types and the theory behind variant calling

Materials:

• ‘Variant calling’ slides

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Variant calling and filtering through short-read sequencing (SNPs and indels) – practical

Trainers: Raheleh Rahbari and Rashesh Sanghvi

Overview: This session addresses variant calling and filtering, going into more depth about the anatomy of a VCF file, and how to use it.

Learning outcomes:

By the end of this session you will be able to:

• Define variant calling and filtering
• Recall the different components of a VCF file and their purpose

Materials:

• Practical session materials

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Variant calling: SVs & CNVs

Trainers: Maxime Tarabachi

Overview: This lecture provides an overview on Structural variants and Copy number variants in genome analysis. The practical provides training on copy-number calling using ASCAT and structural variant calling.

Learning outcomes:

By the end of this session you will be able to:

• Define structural and copy number variants
• Identify structural and copy number variants using ASCAT and GRIDSS2 respectively

Materials:

• ‘Variant calling’ presentation slides
• Practical exercises guide
• Practical session materials:
  • Material for main CNV practical exercises: Data for the CNV practical comes from the github ASCAT page
  • Material for exercises with chromosome 3