ArticleGigaScience2022
xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- De Novo Complex Genomic Rearrangement Spanning 2q31.1 in a Proband With Congenital Malformations: Genotype-Phenotype Correlation and Development of a CGR Detection Pipeline.American journal of medical genetics. Part A · 2026Article
- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Expanding the Clinical and Molecular Spectrum ofmedRxiv : the preprint server for health sciences · 2025Article
- Genomic rare variant mechanisms for congenital cardiac laterality defect: A digenic model approach.American journal of human genetics · 2025Article
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- Single cell RNA-seq: a novel tool to unravel virus-host interplay.Virusdisease · 2024Review
- HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.Nucleic acids research · 2024Article
- The impact of the Turkish population variome on the genomic architecture of rare disease traits.Genetics in medicine open · 2024Article
- Combined bioinformatic and splicing analysis of likely benign intronic and synonymous variants reveals evidence for pathogenicity.Genetics in medicine open · 2024Article
- Identification of Rare Variants Involved in High Myopia Unraveled by Whole Genome Sequencing.Ophthalmology science · 2023Article
- CRISPR-Cas9 correction of a nonsense mutation inMolecular therapy. Methods & clinical development · 2023Article
- Whole genome sequencing forHGG advances · 2023Article
- A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly.American journal of medical genetics. Part A · 2023Article
- The performance of genome sequencing as a first-tier test for neurodevelopmental disorders.European journal of human genetics : EJHG · 2023Article
- xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments.GigaScience · 2022Article
- The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation.Genome medicine · 2022Article
- Genome Sequencing in the Parkinson Disease Clinic.Neurology. Genetics · 2022Article
- De novo mutations in children born after medical assisted reproduction.Human reproduction (Oxford, England) · 2022Observational
- Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station.Scientific reports · 2022Article
- Article
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14 authors.
Funding
Abstract
backgroundThe growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA variation, especially considering that curated high-confidence variant call sets frequently used to validate these methods are generally developed from the analysis of comparatively small and homogeneous sample sets.
findingsWe have developed xAtlas, a single-sample variant caller for single-nucleotide variants (SNVs) and small insertions and deletions (indels) in NGS data. xAtlas features rapid runtimes, support for CRAM and gVCF file formats, and retraining capabilities. xAtlas reports SNVs with 99.11% recall and 98.43% precision across a reference HG002 sample at 60× whole-genome coverage in less than 2 CPU hours. Applying xAtlas to 3,202 samples at 30× whole-genome coverage from the 1000 Genomes Project achieves an average runtime of 1.7 hours per sample and a clear separation of the individual populations in principal component analysis across called SNVs.
conclusionsxAtlas is a fast, lightweight, and accurate SNV and small indel calling method. Source code for xAtlas is available under a BSD 3-clause license at https://github.com/jfarek/xatlas.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.