An Introduction to the analysis of the next-generation sequencing data

Course date: 14 April 2014 - 18 April 2014
Location: Erasmus MC, Faculty bldg

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The course An Introduction to the analysis of the next-generation sequencing data is organized under auspices of the Postgraduate School Molecular Medicine and the Nihes research school.

Registration for this course can be done via the Nihes website: http://nihes.nl/application-admission/application-admission-short-courses/
Please direct all questions concerning registration to Nihes.

Introduction
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 (e.g. PLINK)
  • Single variant and Collapsed genotype analyses with various tools (e.g. seqMeta, RAREMETAL, RVtest, SKAT, RVtdt and CMC)
  • 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
  • Imputation of sequence variants

Prerequisite knowlegde
The course requires working with command line in a LINUX operating system; experience in working with LINUX will be useful. The course assumes that the students are knowledgeable in the field of genetic association analysis and therefore does not aim to teach the statistics behind the software tools that will be used during the course.

More information
Course coordinator: Dr. N. Amin (n.amin@erasmusmc.nl)

Registration for this course can be done via the Nihes website: http://nihes.nl/application-admission/application-admission-short-courses/
Please direct all questions concerning registration to Nihes.



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