Comparison of bioinformatics programs for analysis of single nucleotide variants

Agnieszka Skarzyńska; Magdalena Pawełkowicz; Wojciech Pląder

doi:10.1117/12.2501342

1 October 2018 Comparison of bioinformatics programs for analysis of single nucleotide variants

Agnieszka Skarzyńska, Magdalena Pawełkowicz, Wojciech Pląder

Proceedings Volume 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018; 1080834 (2018) https://doi.org/10.1117/12.2501342
Event: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 2018, Wilga, Poland

Abstract

Changes in genomic sequence might influence the gene expression, protein function and, what is related to phenotype of the organism. The Next Generation Sequencing provides a big amount of data that could be used in predicting the single nucleotide variants between analyzed and reference genome. Herein we compare three tools for predicting the structural variants: Freebayes, GATK toolkit and DeepVariant. Predictions with usage of each program were made on cucumber lines and the results were compared. Our analysis indicates that in order to obtain more precise and reliable variant predictions it is worth to use more than one program for detecting polymorphisms and cross-check the results.

Citation Download Citation

Agnieszka Skarzyńska, Magdalena Pawełkowicz, and Wojciech Pląder "Comparison of bioinformatics programs for analysis of single nucleotide variants", Proc. SPIE 10808, Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, 1080834 (1 October 2018); https://doi.org/10.1117/12.2501342

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