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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Use modern Python libraries and applications to solve real-world computational biology problems

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Product type Paperback
Published in Sep 2022
Publisher Packt
ISBN-13 9781803236421
Length 360 pages
Edition 3rd Edition
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Table of Contents (15) Chapters Close

Preface 1. Chapter 1: Python and the Surrounding Software Ecology 2. Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib FREE CHAPTER 3. Chapter 3: Next-Generation Sequencing 4. Chapter 4: Advanced NGS Data Processing 5. Chapter 5: Working with Genomes 6. Chapter 6: Population Genetics 7. Chapter 7: Phylogenetics 8. Chapter 8: Using the Protein Data Bank 9. Chapter 9: Bioinformatics Pipelines 10. Chapter 10: Machine Learning for Bioinformatics 11. Chapter 11: Parallel Processing with Dask and Zarr 12. Chapter 12: Functional Programming for Bioinformatics 13. Index 14. Other Books You May Enjoy

Using Mendelian error information for quality control

So, how can we infer the quality of calls using Mendelian inheritance rules? Let’s look at expectations for different genotypical configurations of the parents:

  • For a certain potential bi-allelic SNP, if the mother is AA and the father is also AA, then all offspring will be AA.
  • If the mother is AA and the father TT, then all offspring will have to be heterozygous (AT). They always get an A from the mother, and they always get a T from the father.
  • If the mother is AA and the father is AT, then the offspring can be either AA or AT. They always get an A from the mother, but they can get either an A or a T from the father.
  • If both the mother and the father are heterozygous (AT), then the offspring can be anything. In theory, there is not much we can do here.

In practice, we can ignore mutations, which is safe to do with most eukaryotes. The number of mutations (noise, from our perspective) is several...

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