Introduction to Variant Analysis of NGS Data


to be determined (2 days)


The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK

Application deadline:

to be determined

Cancellation deadline:

to be determined


12 (selection of applicants)

Registration fee:

to be determined


Bert Overduin

Next generation sequencing (NGS) of both whole genomes and exomes is a valuable method for the discovery of variants that underlie Mendelian disorders as well as complex disorders. While the sequencing itself has become largely routine, the analysis of the enormous amounts of generated data still poses considerable challenges. The aim of this 2-day workshop is to familiarise researchers with and to initiate them in the variant analysis of NGS data by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs (e.g. FastQC, FastqMcf, Bowtie2, TopHat2, Picard, RSeQC, samtools, IGV, GATK, DeNovoGear, MuTect, RVtests, VEP, SnpEff, ANNOVAR) will be used. The workshop will be focused on human and in the practicals data sets from human will be used.

"This was a fantastic workshop. The organisers were both incredibly helpful and patient." (October 2015)


Dr. Marta Bleda (Computational Biologist, University of Cambridge)
Dr. Ignacio Medina (Computational Biologist, University of Cambridge)

Workshop format

The workshop consists of presentations, demos and hands-on tutorials.

Who should attend

Graduates, postgraduates, or PIs, who want to learn how to do variant analysis of next generation sequencing data.


A general understanding of molecular biology and genomics, and elementary skills in computer usage are required.

Covered topics

Day 1

Introduction to Next Generation Sequencing
Introduction to Linux
Quality control and data pre-processing
Mapping to a reference genome
Mapping quality control
Visualisation of mapped reads

Day 2

Germline variant calling
Visualisation of variants
Somatic variant calling and discovery of de novo mutations
Variant filtering
Variant annotation
Rare variant association tests: single variant and burden analysis
Troubleshooting and help with own data