Table of Contents
Exercise 8
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.
Solutions
A. Individual filters
- 36424 SNVs, 3556 INDELs, 16 MNVs, 4 SVs, 0 CNVs
- Candidate variants: 0
- Candidate variants: 2214
B. Progressive selection
- 2214 → 705 → 1