This course provides an introduction to working with Next-Generation Sequencing (NGS) data. It targets individuals who have access to NGS data and want to learn how to work with this data and what the possibilities and limitations of NGS are. Lectures will be complemented with practical sessions in which the student will gain hands-on experience with various tools and techniques.Subjects that will be covered include:
NGS: an introduction to methodology and techniques;
Basic statistics of NGS data, e.g. coverage;
Aligning the sequence reads;
Calling sequence and structural variants;
Dealing with various file formats (samtools, VCFtools, GATK);
Annotating sequence and structural variants;
Evaluating functional effects of the genetic variants on proteins;
Conversion to other formats;
Single variant and Collapsed genotype analyses with various tools (e.g. seqMeta, RAREMETAL and RVtest);
Finding variants with recessive effects and compound heterozygosity;
Search for rare variants in families and population based studies for complex phenotypes;
Search for rare variants in Mendelian disorders, and
Imputation of sequence variants.
