Table of Contents
Exercise 6
Data description: cases vs. controls
Working plan
How many variants do you detect for each scenario?
A. Individual filters
- Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
- Reference for all controls and homozygous variant for all cases.
- Reference for all controls and heterozygous variant for all cases.
B. Progressive selection
- 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.