Alignment
All data and files for this section can be found in the EBI training FTP.
SAM/BAM file formats
Trainers: Chiara Batini
Overview: This lecture covers the SAM, BAM and CRAM file formats in more detail, with a focus on how to manipulate and interrogate SAM and BAM files.
Learning outcomes:
By the end of this session you will be able to:
- Recall the main features of SAM, BAM, CRAM files
Materials:
Introduction to BASH, loops, and variables
Trainers: Kayesha Coley
Overview: This lecture covers BASH commands, loops and variables in UNIX command line for sequence processing, and a practical on BASH scripting.
Learning outcomes:
By the end of this session you will be able to:
- Recall code used to conduct loops and commands in UNIX
- Apply BASH scripting to sequence processing
Materials:
BAM refinement, QC & visualisation
Trainers: Chiara Batini
Overview: This lecture covers BAM refinement, BAM QC, BAM visualisation and GATK best practices.
Learning outcomes:
By the end of this session you will be able to:
- List the steps to refine, assess quality and visualise BAM files
- Recall GATK best practices for sequencing
Materials:
Variant calling
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: