EMBL Advanced Course - Variant Calling from Genomic Sequencing Data

Date: 18-Jul-2011 2:00 CEST to -

Contact: Petra Lindemann

Methods, Tools and Algorithms for Calling SNPs, Short InDels and Large Structural Variants from Whole-Genome Sequencing Data

This course covers methods and algorithms to call genomic alterations in a whole-genome, next-generation sequencing data set. We will focus on algorithms to map reads, call single nucleotide polymorphisms, short indels and structural variants. The course offers both lectures and hands-on examples. The lectures will focus on fundamental algorithms and data structures for next-generation sequencing data analysis, including

  • Read mapping

  • Realignment and consensus calling

  • SNP calling, filtering and annotation

  • Read-depth methods for large-scale genomic aberrations

  • Structural variant calling using paired-end and split-read alignment methods

  • Assembly methods

During the hands-on sessions, participants will carry out some of the above analyses on a real world whole-genome sequencing data set.


Participants should have a strong computational background. Familiarity with the Linux command line and computer programming is required. Knowledge of next-generation sequencing technology and its biological applications is assumed. Some experience with R for statistical a nalysis is beneficial.