Table of Contents

Exercise 10

Data description




Working plan

We have several candidate profiles of mutations to explore:

How many variants do you detect for each scenario?

A. Individual filters

  1. Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
  2. Recessive heritage
  3. Dominant heritage (father is affected).
  4. For this chromosome: 5
  5. Evaluate these regions at the same time: 5,6:10000-500000
  6. For theses genes: SDHA,AHRR
  7. Are there variants for these SNPs: rs6682385,rs75478250,rs147502335?
  8. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African population in 1000 Genomes phase 1
  9. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African population in 1000 Genomes phase 3
  10. Variants with MAF (Minimum Allelic Frequency) < 0.001 for African American population in ESP 6500


B. Progressive selection

  1. There are clear information about our candidate variants:
    • Recessive heritage
    • Chromosome 1
    • SNV
    • Variants with MAF (Minimum Allelic Frequency) < 0.001 for all populations in 1000 Genomes phase 1
      • How many variants do you have including both characteristics?
      • Download these final results in a csv file



Solutions

A. Individual filters

  1. 36424 SNVs, 3552 INDELs, 19 MNVs, 3 SVs, 0 CNVs
  2. Candidate variants: 980
  3. Candidate variants: 1107
  4. Candidate variants: 1826
  5. Candidate variants: 1832
  6. Candidate variants: 16
  7. Candidate variants: 2
  8. Candidate variants in 1000 Genomes, phase 1: 11925
  9. Candidate variants in 1000 Genomes, phase 3: 12894
  10. Candidate variants in African American MAF population: 21319

B. Progressive selection

  1. 980 → 106 → 94 → 14