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: Chiara Batini

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

Trainers: Chiara Batini

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:

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: