Assessing-Variant-Calling-Pipelines-Mini-Project

Overview

This mini-project involves assessing various variant calling pipelines inorder to come up with an optimized/standardized variant calling pipeline for analyzing insect and pathogen data.

Contributors

• Allan Okeyo
• Joyce Wangari

Mentors

• Dr. Caleb Kibet
• Ruth Nanjala
• Andrew Espira
• Hebrew Simon
• Rose Wambui

Vision

To design a standard variant calling pipeline that is effective and reliable for analyzing insect and pathogen data, that will be adopted across various regions of the world.

Mission

To evaluate existing varinat calling pipelines, fill in existing gaps and modify the pipelines to suit anlysis of insect and pathogen data.

Evaluation criteria

• How easy are they to set up and use? Do they provide accessible documentation and tutorials?
• Are they fast and easily scalable based on available compute resources?
• Can they scale to the cloud?
• Can they be used on a variety of data, including insects, pathogens and microbes (virus and bacteria)
• Are they implemented in the latest specifications and versions of the tools? For example, Whether the pipeline implements Nextflow DSL2 syntax and docker or singularity containers
• Are they well and regularly maintained? When were they updated last?

Background information

What is Genetic Variation?

• This refers to the difference in the DNA sequences between individuals in a population.
• They can occur in both the germ cells (sperm and egg) and body cells(somatic).
• Germline variations are of more importance relative to somatic varince since germline variations can be inherited to successive generations affecting population dynamics and ultimately population evolution.

Types of Genetic Variation

1. Single Base pair substitution

• These are also known as single nucleotide polymorphisms (SNPs) and involve one nucleic acid substitution

• They can be used to predict how an individual would respond to drugs of a particular class, susceptibilty to certain environmental stimulus and well predisposal to certain diseases

• They can be helpful in tracking inheritable of diseases within a family.

• They are of two types:

  Transition: This involves the interchange between purines; between Adenine and Guanine and interchange between pyrimidines; between Cytosine and Thymine

  Transversion: This involves interchange between a purine and a pyrimidine for example, between Adenine and Cytosine

  2. Insertion or deletion (Indels)

• These are classified as small genetic mutations and involve the insertion or deletion of nucleotide bases and can range from one to hundreds of base-pairs in length

  3. Structural Variation

• This involves genetic variation that occur over a larger DNA sequence it includes copy number variation and chromosomal rearrangements common types of structural variations include: deletion, inversion,insertion, duplication, and copy number variation.

  Copy Number Variation

  • These are variations in the DNA that affects a large chank of the DNA, leading to repeats of some sections of DNA.
  • Can occur as a result of duplication or deletion events in the DNA sequence.
  • Are of importance in determining disease phenotype and population diversity

  What is Variant calling?

  Variant calling is the process by which variants are identified from sequence data.

  Variant calling intuition

The goal is to obtain a vcf (variant calling format) file that shows variants for all individuals in a given population

Intuition

1. Starting point-raw sequences
2. Know where they align
3. Know the genotype for each position
4. Look across all samples and determine which sites are variants.

Work plan

Here is a link to our project road map