Table of Contents

Exercise 6

Data description: cases vs. controls




Working plan

How many variants do you detect for each scenario?

A. Individual filters

  1. Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
  2. Reference for all controls and homozygous variant for all cases.
  3. Reference for all controls and heterozygous variant for all cases.


B. Progressive selection

  1. We have several clues about our candidate variants:
    • Reference for all controls and heterozygous variant for all cases.
    • We search variants with MAF < 0.001 (for all populations in 1000 Genomes phase 3) because it is a rare disease.
    • Chromosome 13
      • How many variants do you have including both characteristics?
      • Select this variant and visualize it from the Genomic browser.