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
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
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.