Comparative analysis of whole-genome sequencing pipelines to minimize false negative findings
| Autor: | Dhong-Geon Won, Sek Won Kong, Honglan Li, Carles Hernandez-Ferrer, In-Hee Lee, Kyu-Baek Hwang, Jose A. Negron |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Genotype Computer science Concordance Black People lcsh:Medicine Computational biology Genome Polymorphism Single Nucleotide White People Article 03 medical and health sciences 0302 clinical medicine Gene Frequency Humans 1000 Genomes Project lcsh:Science Alleles Whole genome sequencing Multidisciplinary Whole Genome Sequencing Genome Human lcsh:R Genetic Variation High-Throughput Nucleotide Sequencing Genomics Pipeline (software) 3. Good health Pipeline transport Minor allele frequency 030104 developmental biology Haplotypes lcsh:Q 030217 neurology & neurosurgery Algorithms Reference genome |
| Zdroj: | Scientific Reports, Vol 9, Iss 1, Pp 1-10 (2019) Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-019-39108-2 |
| Popis: | Comprehensive and accurate detection of variants from whole-genome sequencing (WGS) is a strong prerequisite for translational genomic medicine; however, low concordance between analytic pipelines is an outstanding challenge. We processed a European and an African WGS samples with 70 analytic pipelines comprising the combination of 7 short-read aligners and 10 variant calling algorithms (VCAs), and observed remarkable differences in the number of variants called by different pipelines (max/min ratio: 1.3~3.4). The similarity between variant call sets was more closely determined by VCAs rather than by short-read aligners. Remarkably, reported minor allele frequency had a substantial effect on concordance between pipelines (concordance rate ratio: 0.11~0.92; Wald tests, P |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
| Nepřihlášeným uživatelům se plný text nezobrazuje | K zobrazení výsledku je třeba se přihlásit. |