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Comparing Copy Number Variations and SNPs

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Read trimming has minimal effect on bacterial SNP-calling accuracy.

Stephen J Bush¹

¹Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Microbial Genomics

|December 17, 2020

Summary

Read trimming offers minimal improvement for variant calling accuracy in bacterial genomics. This study suggests trimming is often unnecessary, saving time and resources in large-scale analyses.

Keywords:

SNP calling read pre-processing read trimming variant calling

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Area of Science:

Genomics and Bioinformatics
Computational Biology
Microbial Genomics

Background:

Read alignment is crucial for variant calling in genomic pipelines.
Pre-processing raw sequencing reads via trimming is common practice to improve accuracy.
The efficacy of read trimming for variant calling remains debated, with limited systematic evaluations.

Purpose of the Study:

To systematically evaluate the impact of read trimming on variant calling accuracy and completeness.
To assess the necessity and benefits of read trimming in large-scale bacterial genomic analyses.
To compare the performance of different read-trimming utilities.

Main Methods:

Evaluated four trimming utilities (Atropos, fastp, Trim Galore, Trimmomatic) on 17 Gram-negative bacterial genomes.
Assessed impact on SNP-calling pipelines with varying stringencies.
Re-analyzed over 6500 public sequencing datasets from E. coli, M. tuberculosis, and S. aureus.

Main Results:

Read trimming provided only small, statistically insignificant increases in SNP-calling accuracy.
Variant base calls remained consistent (>98.8% for SNPs, >91.9% for indels) with or without trimming.
Trimming significantly reduced the proportion of mixed calls, indicating a potential decrease in false positives.

Conclusions:

Read trimming offers marginal benefits for SNP and indel calling accuracy in bacterial genomics.
Trimming may be necessary only when small differences in call numbers or false call rates are critical.
Routine read trimming may not be a practical necessity for many variant calling pipelines.