ArticleBioinformatics (Oxford, England)2018
geck: trio-based comparative benchmarking of variant calls.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing.Molecular ecology resources · 2025Article
- Understanding Mendelian errors in SNP arrays data using a Gochu Asturcelta pig pedigree: genomic alterations, family size and calling errors.Scientific reports · 2022Article
- PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data.Briefings in bioinformatics · 2021Review
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.Frontiers in genetics · 2020Review
- Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Comparing complex variants in family trios.Bioinformatics (Oxford, England) · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Motivation: Classical methods of comparing the accuracies of variant calling pipelines are based on truth sets of variants whose genotypes are previously determined with high confidence. An alternative way of performing benchmarking is based on Mendelian constraints between related individuals. Statistical analysis of Mendelian violations can provide truth set-independent benchmarking information, and enable benchmarking less-studied variants and diverse populations. Results: We introduce a statistical mixture model for comparing two variant calling pipelines from genotype data they produce after running on individual members of a trio. We determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method is able to estimate differential precision and recall between the two pipelines with 10-3 uncertainty. Availability and implementation: The Python library geck, and usage examples are available at the following URL: https://github.com/sbg/geck, under the GNU General Public License v3. Supplementary information: Supplementary data are available at Bioinformatics online.
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