Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans

Conclusion In this study, we demonstrated that different pipelines have a specific tendency to detect the DNSNVs in the genomic regions with different GC contents. GATK performed better on detecting the DNSNVs in the low GC-content region while RTG and VarScan are better suited for detecting the DNSNVs in the high GC-content region. To refine the calling results for single pipeline, the read coverage at the mutation positions of the son’s genome and the parents’ genomes can be considered as an effective index to identify DNSNVs with high confidence. Our findings would be useful for the community to choose the appropriate pipelines and obtain the calling results with high confidence when discovering the de novo mutations for the genetic diseases. Author Contributions ZW designed the experiments. YL, LH, YZ, and YH performed the data analysis. ZW wrote the initial version of manuscript. YZ, YL, and ML prepared all the figures. ZW, CL, and XP discussed the results and revised the manuscript. All authors contributed to discussions regarding the results and the manuscript. Funding This project was supported by grants from the National Natural Science Foundation of China (Nos. 21575094 and 21573151) and NSAF (No. U1730127). Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Supplementary Material The Suppleme...
Source: Frontiers in Pharmacology - Category: Drugs & Pharmacology Source Type: research