Tools for Analyzing Genetic Variants from Sequencing Data – Case Study: Short Tandem Repeats

In this webinar, presented by Melissa Gymrek, PhD, Broad Institute of MIT and Harvard, you will learn:

  • How to go from raw next generation sequencing data to high quality genotypes.
  • How to use lobSTR, a tool we developed for profiling short tandem repeats from short reads.
  • Effective ways to visualize sequence alignments and variant calls using popular genome browsers.


Every individual harbors millions of genetic variants, many of which may contribute to phenotype. As the cost of sequencing has plummeted, we now have the opportunity to profile this variation across thousands of individuals. Here I will provide an overview of the workflow to analyze various types of genetic variation, starting from raw sequencing data and ending with high quality genotypes. I will first present state of the art methods for mapping raw sequences to the human reference genome and calling single nucleotide polymorphisms (SNPs) across one or thousands of samples. I will then briefly describe tools for genotyping more complex variant types, focusing on STRs as a case study. Finally, I will give an overview of tools for visualizing sequencing data and for downstream analysis of genotypes.