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

Freed, Donald; Aldana, Rafael; Ja, Weber; Js, Edwards

doi:10.1101/115717

Cited by 195 publications

(167 citation statements)

References 28 publications

(25 reference statements)

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“…Reads were sorted and duplicates were removed with Picard, version 2.17.5.; base quality score recalibration was then performed with the Genome Analysis Toolkit (GATK), v3.8-0-ge9d806836. Variant calling and joint genotyping were done with the Haplotyper and Genotyper tools from Sentieon v201711.01, a toolkit containing modules that are mathematically equivalent to their counterparts in the GATK (Freed et al, 2017). SNP and indel recalibration were performed on the joint genotyped VCF file.…”

Section: Wgs Variant Callingmentioning

confidence: 99%

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex

et al. 2020

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All available non-identifying information was recorded for each specimen in Table S1. In total, 176 postmortem brain specimens (104 male, 72 female; postmortem interval of 21.7 ± 15.9 (mean ± SD) hours and pH, 6.41 ± 0.35) ranging in age from 6 post-conception weeks (PCW) to 20 postnatal years (PY) ( Figure 1 and Table S1) were included in this study. Fetal age was extrapolated based on the date of the mother's last menstruation, characteristics of the fetus noted upon ultrasonography scanning, foot length of the fetus, and visual inspection. The postmortem interval (PMI) was defined as hours between time of death and time when tissue samples were frozen. METHOD DETAILS Tissue dissectionTissue was dissected as described previously (Kang et al. 2011). Samples collected from 6 -9 PCW specimens contained the entire thickness of the cerebral wall. Samples collected from 12 -22 PCW specimens contained the cortical plate. Samples from 35 PCW -20 PY specimens were dissected such that the entire gray matter (layer 1-6) and part of the underlying subplate (4 -12 postnatal months) or white matter (1 -20 PY) were collected. RNA extraction and quality assessmentTotal RNA was extracted using mirVana kit (Ambion) with some modifications, as given in the following text, to the manufacturer's protocol, as described below. Each tissue sample was

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Section: Wgs Variant Callingmentioning

confidence: 99%

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex

et al. 2020

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“…GLnexus has a declarative configuration scheme enabling it to interpret gVCF inputs from several upstream variant calling tools and accommodate others in the future. In addition to GATK HaplotypeCaller used above, suitable configurations are included for Platypus [7], xAtlas [21], DeepVariant [22], Sentieon DNAseq [23], and Edico DRAGEN, though not all have been calibrated to the same degree. Additionally, GLnexus can be operated in a simplified mode to merge input gVCFs but skip QC filtering and genotype recalculation.…”

Section: Availabilitymentioning

confidence: 99%

GLnexus: joint variant calling for large cohort sequencing

Lin

Rodeh

Penn

et al. 2018

Preprint

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As ever-larger cohorts of human genomes are collected in pursuit of genotype/phenotype associations, sequencing informatics must scale up to yield complete and accurate genotypes from vast raw datasets. Joint variant calling, a data processing step entailing simultaneous analysis of all participants sequenced, exhibits this scaling challenge acutely. We present GLnexus (GL, Genotype Likelihood), a system for joint variant calling designed to scale up to the largest foreseeable human cohorts. GLnexus combines scalable joint calling algorithms with a persistent database that grows efficiently as additional participants are sequenced. We validate GLnexus using 50,000 exomes to show it produces comparable or better results than existing methods, at a fraction of the computational cost with better scaling. We provide a standalone opensource version of GLnexus and a DNAnexus cloudnative deployment supporting very large projects, which has been employed for cohorts of >240,000 exomes and >22,000 whole-genomes.

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“…We used the Sentieon variant caller 18 (Mountain View, CA) v201711 to implement the GATK tools, following the GATK Best Practices for variant detection. 19 We generated a genome variant call format (gVCF) file for each sample using Sentieon Haplotyper and then performed joint variant calling on all eight samples with Sentieon GVCFtyper.…”

Section: Exome Sequencing and Germline Variant Callingmentioning

confidence: 99%

Genetic risk of cholangiocarcinoma is linked to the autophagy gene ATG7

Greer

Ögmundsdóttir

Chen

et al. 2019

Preprint

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Cholangiocarcinoma is an aggressive cancer originating from the bile duct. Although cholangiocarcinoma does occur in families, to date no specific causative gene has been identified. We identified ATG7 as a cancer susceptibility gene using a joint genetic analysis of an extended pedigree with familial cholangiocarcinoma in combination with a population genetic association study. Affected family members had a germline mutation (c.2000C>T [p.Arg659*]) in the autophagy related gene, ATG7, and all of the affected individuals had cholangiocarcinoma tumors harboring somatic genomic deletions of ATG7. From a population genetic study, we identified a germline polymorphism of ATG7 (c.1591C>G [p.Asp522Glu]) associated with increased risk of cholangiocarcinoma. The autophagy substrate p62 demonstrated a higher accumulation in tumors of p.Asp522Glu carriers compared with noncarriers indicating defective autophagy. To determine whether the germline ATG7 mutation had functional consequences, we developed an ATG7-deficient cholangiocyte cell line, derived from human bile duct, to test for autophagy-mediated lipidation activity. The germline mutation from the familial cholangiocarcinoma demonstrated a lack of lipidation activity compared to the wildtype ATG7. Moreover, in zebrafish embryos depleted of atg7, a reproducible necrotic headphenotype was rescued by injection of wildtype ATG7 but not mutant ATG7. Our findings point to ATG7 as a causative genetic risk factor for cholangiocarcinoma and implicate autophagy as a novel cancer driver mechanism.

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

Cited by 195 publications

References 28 publications

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex

GLnexus: joint variant calling for large cohort sequencing

Genetic risk of cholangiocarcinoma is linked to the autophagy gene ATG7

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