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The Sentieon Genomics Tools - A fast and accurate solution to variant calling from next-generation sequence data

https://doi.org/10.1101/115717
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature07484openalex-snapshot
The diploid genome sequence of an Asian individual
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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
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The contribution of de novo coding mutations to autism spectrum disorder
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A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature15816openalex-snapshot
Building the foundation for genomics in precision medicine
inferredcites →https://doi.org/10.1038/nbt.2514openalex-snapshot
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
inferredcites →https://doi.org/10.1038/ng.3034openalex-snapshot
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
inferredcites →https://doi.org/10.1038/ng.3036openalex-snapshot
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1038/ng.499openalex-snapshot
Exome sequencing identifies the cause of a mendelian disorder
inferredcites →https://doi.org/10.1038/ng.806openalex-snapshot
A framework for variation discovery and genotyping using next-generation DNA sequencing data
inferredcites →https://doi.org/10.1038/nmeth.3407openalex-snapshot
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
inferredcites →https://doi.org/10.1038/nrg.2016.86openalex-snapshot
Towards precision medicine
inferredcites →https://doi.org/10.1038/nrg3555openalex-snapshot
Rare-disease genetics in the era of next-generation sequencing: discovery to translation
inferredcites →https://doi.org/10.1056/nejmoa1311037openalex-snapshot
DNA Sequencing versus Standard Prenatal Aneuploidy Screening
inferredcites →https://doi.org/10.1056/nejmp1006304openalex-snapshot
The Path to Personalized Medicine
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot
Mapping short DNA sequencing reads and calling variants using mapping quality scores
inferredcites →https://doi.org/10.1101/gr.088013.108openalex-snapshot
SNP detection for massively parallel whole-genome resequencing
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1111/cge.12732openalex-snapshot
Diagnostic odyssey in severe neurodevelopmental disorders: toward clinical whole‐exome sequencing as a first‐line diagnostic test
inferredcites →https://doi.org/10.1126/science.1208130openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.aaa4971openalex-snapshot
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inferredcites →https://doi.org/10.1126/scitranslmed.aaf7314openalex-snapshot
A research roadmap for next-generation sequencing informatics
inferredcites →https://doi.org/10.1158/2326-6066.cir-13-0022openalex-snapshot
Getting Personal with Neoantigen-Based Therapeutic Cancer Vaccines
inferredcites →https://doi.org/10.1371/journal.pbio.1002195openalex-snapshot
Big Data: Astronomical or Genomical?
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7287/peerj.preprints.1672v1openalex-snapshot
Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results
inferredcites →https://doi.org/10.7287/peerj.preprints.1672v2openalex-snapshot
Sentieon DNA pipeline for variant detection - Software-only solution, over 20× faster than GATK 3.3 with identical results

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1038/s41421-020-00231-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41422-025-01200-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41438-020-0330-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41467-021-25440-7openalex-snapshot
Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation
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The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma
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inferred← citeshttps://doi.org/10.1038/s41467-023-43985-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1038/s41467-025-61712-2openalex-snapshot
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A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia
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Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study
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Sequencing by avidity enables high accuracy with low reagent consumption
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High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement
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The highly allo-autopolyploid modern sugarcane genome and very recent allopolyploidization in Saccharum
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Whole-genome sequencing resources of 301 indigenous Tibetan sheep from the Himalayan region
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Reliable variant calling during runtime of Illumina sequencing
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Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma
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Germline variants of ATG7 in familial cholangiocarcinoma alter autophagy and p62
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RNA-seq and whole-genome re-sequencing reveal Micropterus salmoides growth-linked gene and selection signatures under carbohydrate-rich diet and varying temperature
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Unveiling population structure in South Pacific albacore: insights from genetics and growth
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Whole exome sequencing and 12-SNP LDL polygenic score in South Indian patients with familial hypercholesterolemia
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Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning
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Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel
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Trans-ethnic genome-wide association study of severe COVID-19
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Low-viscosity matrix suspension culture enables scalable analysis of patient-derived organoids and tumoroids from the large intestine
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Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids
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BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes
inferred← citeshttps://doi.org/10.1038/s42003-022-04374-wopenalex-snapshot
Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats
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EPI-SauriCas9-based mouse ovarian cancer models recapitulating pten deletion in patients
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Population genomics of Quercus gilva provides insights into the conservation of fengshui forests
inferred← citeshttps://doi.org/10.1038/s42003-026-10840-6openalex-snapshot
Identifying causal genetic variants for high-altitude adaptation through blood eQTL analysis in plateau populations
inferred← citeshttps://doi.org/10.1038/s44276-025-00155-0openalex-snapshot
Whole genome sequencing and single-cell transcriptomics identify KMT2D inactivation as a potential new driver for pituitary tumors: a case report
inferred← citeshttps://doi.org/10.1055/s-0040-1713850openalex-snapshot
Next-Generation Sequencing in a Cohort of Asian Indian Patients with the Duchenne Muscular Dystrophy Phenotype: Diagnostic Yield and Mutation Spectrum
inferred← citeshttps://doi.org/10.1055/s-0044-1790245openalex-snapshot
Phenotypic Heterogeneity in ORAI-1-Associated Congenital Myopathy
inferred← citeshttps://doi.org/10.1080/00207454.2022.2100774openalex-snapshot
Congenital myasthenic syndrome: a tale of two siblings
inferred← citeshttps://doi.org/10.1080/01443615.2022.2049718openalex-snapshot
Heterochromatin extension: a possible cytogenetic fate of primary amenorrhea along with normal karyotype
inferred← citeshttps://doi.org/10.1093/bib/bbaa148openalex-snapshot
Benchmarking variant callers in next-generation and third-generation sequencing analysis
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf085openalex-snapshot
Benchmarking accelerated next-generation sequencing analysis pipelines
inferred← citeshttps://doi.org/10.1093/evlett/qraf013openalex-snapshot
Diverging Arabidopsis populations quickly accumulate pollen-acting genetic incompatibilities
inferred← citeshttps://doi.org/10.1093/g3journal/jkae281openalex-snapshot
A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize
inferred← citeshttps://doi.org/10.1093/gbe/evac015openalex-snapshot
Chromosome-Level Genome Assembly of the Green Peafowl (Pavo muticus)
inferred← citeshttps://doi.org/10.1093/gbe/evad069openalex-snapshot
A Long-Standing Hybrid Population Between Pacific and Atlantic Herring in a Subarctic Fjord of Norway
inferred← citeshttps://doi.org/10.1093/gigascience/giae034openalex-snapshot
Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers
inferred← citeshttps://doi.org/10.1093/gigascience/giae081openalex-snapshot
Genomic exploration of the endangered oriental stork, Ciconia boyciana , sheds light on migration adaptation and future conservation
inferred← citeshttps://doi.org/10.1093/gigascience/giaf003openalex-snapshot
Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin
inferred← citeshttps://doi.org/10.1093/jhered/esab054openalex-snapshot
Variable Signatures of Selection Despite Conserved Recombination Landscapes Early in Speciation
inferred← citeshttps://doi.org/10.1093/jhered/esaf089openalex-snapshot
Genomic Assessment of Giraffes in North American Collections Highlights Conservation Challenges
inferred← citeshttps://doi.org/10.1093/nar/gkaa923openalex-snapshot
IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes
inferred← citeshttps://doi.org/10.1093/nar/gkac936openalex-snapshot
IAnimal: a cross-species omics knowledgebase for animals
inferred← citeshttps://doi.org/10.1093/nar/gkad779openalex-snapshot
A high-resolution haplotype-resolved Reference panel constructed from the China Kadoorie Biobank Study
inferred← citeshttps://doi.org/10.1093/pcmedi/pbae007openalex-snapshot
Genome and clonal hematopoiesis stability contrasts with immune, cfDNA, mitochondrial, and telomere length changes during short duration spaceflight
inferred← citeshttps://doi.org/10.1093/sysbio/syad062openalex-snapshot
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation
inferred← citeshttps://doi.org/10.1101/2020.07.23.218602openalex-snapshot
Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes in the ABRF Next-Generation Sequencing Study
inferred← citeshttps://doi.org/10.1101/2021.03.29.437607openalex-snapshot
Epigenetic models predict age and aging in plains zebras and other equids
inferred← citeshttps://doi.org/10.1101/2021.09.09.459637openalex-snapshot
Not so local: the population genetics of convergent adaptation in maize and teosinte
inferred← citeshttps://doi.org/10.1101/2021.12.07.471513openalex-snapshot
Attentive deep learning-based tumor-only somatic mutation classifier achieves high accuracy agnostic of tissue type and capture kit
inferred← citeshttps://doi.org/10.1101/2021.12.12.472266openalex-snapshot
High performance of a GPU-accelerated variant calling tool in genome data analysis
inferred← citeshttps://doi.org/10.1101/2021.12.23.21268291openalex-snapshot
Complete genomic profiles of 1,496 Taiwanese reveal curated medical insights
inferred← citeshttps://doi.org/10.1101/2022.05.20.492556openalex-snapshot
DNAscope: High accuracy small variant calling using machine learning
inferred← citeshttps://doi.org/10.1101/2022.06.01.494452openalex-snapshot
Sentieon DNAscope LongRead – A highly Accurate, Fast, and Efficient Pipeline for Germline Variant Calling from PacBio HiFi reads
inferred← citeshttps://doi.org/10.1101/2022.06.03.494742openalex-snapshot
Processing UMI Datasets at High Accuracy and Efficiency with the Sentieon ctDNA Analysis Pipeline
inferred← citeshttps://doi.org/10.1101/2022.11.25.517889openalex-snapshot
Multi-omics analyses of single cell-derived colorectal cancer organoids reveal intratumor heterogeneity and immune response diversity
inferred← citeshttps://doi.org/10.1101/2023.06.22.546072openalex-snapshot
Unveiling the signaling network of FLT3-ITD AML improves drug sensitivity prediction
inferred← citeshttps://doi.org/10.1101/2023.10.23.562618openalex-snapshot
The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring
inferred← citeshttps://doi.org/10.1101/2023.12.03.569791openalex-snapshot
Tumor-selective effects of active RAS inhibition in pancreatic ductal adenocarcinoma
inferred← citeshttps://doi.org/10.1101/2023.12.20.23300308openalex-snapshot
Imputation of structural variants using a multi-ancestry long-read sequencing panel enables identification of disease associations
inferred← citeshttps://doi.org/10.1101/2024.01.24.577136openalex-snapshot
Optimizing Accuracy and Efficiency in Analyzing Non-UMI Liquid Biopsy Datasets Using the Sentieon ctDNA Pipeline
inferred← citeshttps://doi.org/10.1101/2024.02.28.24303417openalex-snapshot
Identification of Novel Gene variants for Autism Spectrum Disorder in an Indian Patient using Whole Exome Sequencing
inferred← citeshttps://doi.org/10.1101/2024.03.06.583766openalex-snapshot
Adaptive admixture at ACKR1 (the Duffy locus) may have shaped Plasmodium vivax prevalence in Oman
inferred← citeshttps://doi.org/10.1101/2024.09.17.24312241openalex-snapshot
Whole Genome Sequencing and single-cell transcriptomics identify KMT2D as a potential new driver for pituitary adenomas
inferred← citeshttps://doi.org/10.1101/2025.02.26.638035openalex-snapshot
A monophyletic origin of domesticated barley
inferred← citeshttps://doi.org/10.1101/2025.03.03.641227openalex-snapshot
Multiplex-edited mice recapitulate woolly mammoth hair phenotypes
inferred← citeshttps://doi.org/10.1101/2025.10.13.681545openalex-snapshot
Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data
inferred← citeshttps://doi.org/10.1101/2025.10.28.685157openalex-snapshot
Single cell whole genome and transcriptome sequencing links somatic mutations to cell identity and ancestry
inferred← citeshttps://doi.org/10.1101/2025.10.31.685648openalex-snapshot
A comprehensive view of somatic mosaicism by single-cell DNA analysis
inferred← citeshttps://doi.org/10.1101/2025.11.02.685776openalex-snapshot
Adaptive introgression from Pacific herring to Atlantic herring in the brackish Baltic Sea
inferred← citeshttps://doi.org/10.1101/2025.11.14.688541openalex-snapshot
Accelerated and High-Accuracy Variant Calling on Oxford Nanopore Technologies Sequencing Data with the Sentieon DNAscope LongRead and Hybrid Pipelines
inferred← citeshttps://doi.org/10.1101/222307openalex-snapshot
Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel
inferred← citeshttps://doi.org/10.1101/250647openalex-snapshot
TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering
inferred← citeshttps://doi.org/10.1101/262196openalex-snapshot
How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio
inferred← citeshttps://doi.org/10.1101/324392openalex-snapshot
Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly
inferred← citeshttps://doi.org/10.1101/343970openalex-snapshot
GLnexus: joint variant calling for large cohort sequencing
inferred← citeshttps://doi.org/10.1101/798264openalex-snapshot
A catalog of homoplasmic and heteroplasmic mitochondrial DNA variants in humans
inferred← citeshttps://doi.org/10.1101/836767openalex-snapshot
Genetic risk of cholangiocarcinoma is linked to the autophagy gene ATG7
inferred← citeshttps://doi.org/10.1101/gr.245126.118openalex-snapshot
Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
inferred← citeshttps://doi.org/10.1101/gr.247122.118openalex-snapshot
Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony
inferred← citeshttps://doi.org/10.1109/bibm.2018.8621573openalex-snapshot
Performance Evaluation of IMP: A Rapid Secondary Analysis Pipeline for NGS Data
inferred← citeshttps://doi.org/10.1109/bibm52615.2021.9669752openalex-snapshot
Evaluation of using WGS/WES to characterize ACMG actionable genes in genetic testing reports
inferred← citeshttps://doi.org/10.1111/age.13183openalex-snapshot
Genome‐wide analysis suggests multiple domestication events of Chinese local pigs
inferred← citeshttps://doi.org/10.1111/bjh.19089openalex-snapshot
Angioimmunoblastic T‐cell lymphoma: Novel recurrent mutations and prognostic biomarkers by cell‐free DNA profiling
inferred← citeshttps://doi.org/10.1111/cts.70416openalex-snapshot
Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial
inferred← citeshttps://doi.org/10.1111/nep.14244openalex-snapshot
INF2 and ROBO2 gene mutation in an Indian family with end stage renal failure and follow‐up of renal transplantation
inferred← citeshttps://doi.org/10.1111/nph.20453openalex-snapshot
Nonadditive regulation confers phenotypic variation in hybrid maize
inferred← citeshttps://doi.org/10.1111/pbi.14018openalex-snapshot
Chromosome‐level wild Hevea brasiliensis genome provides new tools for genomic‐assisted breeding and valuable loci to elevate rubber yield
inferred← citeshttps://doi.org/10.1111/tpj.16038openalex-snapshot
An NBS‐LRR protein in the Rpp1 locus negates the dominance of Rpp1‐mediated resistance against Phakopsora pachyrhizi in soybean
inferred← citeshttps://doi.org/10.1111/tpj.16041openalex-snapshot
High‐resolution sequencing of nine elite upland cotton cultivars uncovers genic variations and breeding improvement targets
inferred← citeshttps://doi.org/10.1111/tpj.70036openalex-snapshot
GWAS and eQTL analyses reveal genetic components influencing the key fiber yield trait lint percentage in upland cotton
inferred← citeshttps://doi.org/10.1111/trf.18401openalex-snapshot
Characterization of blood group variants in an Omani population by comparison of whole genome sequencing and serology
inferred← citeshttps://doi.org/10.1126/sciadv.abm5982openalex-snapshot
Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules
inferred← citeshttps://doi.org/10.1126/sciadv.adf0837openalex-snapshot
Radiogenomic-based multiomic analysis reveals imaging intratumor heterogeneity phenotypes and therapeutic targets
inferred← citeshttps://doi.org/10.1126/science.adf6218openalex-snapshot
Community-wide genome sequencing reveals 30 years of Darwin’s finch evolution
inferred← citeshttps://doi.org/10.1126/science.ads0239openalex-snapshot
A neomorphic protein interface catalyzes covalent inhibition of RAS G12D aspartic acid in tumors
inferred← citeshttps://doi.org/10.1158/1078-0432.ccr-18-3034openalex-snapshot
Comparison of Biomarker Assays for EGFR : Implications for Precision Medicine in Patients with Glioblastoma
inferred← citeshttps://doi.org/10.1167/iovs.66.13.12openalex-snapshot
Hidden Splicing Variants in Inherited Retinal Degeneration: Discovery and Functional Insight
inferred← citeshttps://doi.org/10.1172/jci147834openalex-snapshot
Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19
inferred← citeshttps://doi.org/10.1182/blood.2021010858openalex-snapshot
Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells
inferred← citeshttps://doi.org/10.1186/s12859-019-3169-7openalex-snapshot
Recommendations for performance optimizations when using GATK3.8 and GATK4
inferred← citeshttps://doi.org/10.1186/s12859-021-04452-6openalex-snapshot
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data
inferred← citeshttps://doi.org/10.1186/s12859-023-05596-3openalex-snapshot
Performance analysis of conventional and AI-based variant callers using short and long reads
inferred← citeshttps://doi.org/10.1186/s12859-024-05776-9openalex-snapshot
HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations
inferred← citeshttps://doi.org/10.1186/s12859-025-06184-3openalex-snapshot
A novel simulation tool for low-coverage whole-genome sequencing using multivariate Gaussian mixture models
inferred← citeshttps://doi.org/10.1186/s12864-020-07013-yopenalex-snapshot
Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework
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