JointSNVMix specifications

Information


Unique identifier OMICS_00085
Name JointSNVMix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.8.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Sohrab P. Shah <>

Additional information


https://code.google.com/archive/p/joint-snv-mix/

Publication for JointSNVMix

JointSNVMix in publications

 (24)
PMCID: 5928770
PMID: 29565466
DOI: 10.3892/or.2018.6325

[…] processed for local indel realignment, base quality estimation and recalibration for further analysis., somatic mutation calling was performed. for whole exome data, varscan2 () combined with the jointsnvmix2 () algorithm were used to identify somatic mutations and the candidates were merged, while whole genomic data somatic mutation calling used only the varscan2 algorithm. to reduce […]

PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] are available, radia will include the gene expression data in an integrated analysis to further reduce false positives., joint genotype analysis, adopted by somaticsniper, fasd-somatic, samtools, jointsnvmix2, virmid, snvsniffer, seurat, and caveman , , , , , , , , assumes diploidy in both tumor and normal and evaluates the likelihood of the joint genotypes. variant calling becomes a natural […]

PMCID: 5657037
DOI: 10.1186/s12864-017-4134-3

[…] in the same domain. we compared j48 to somaticseq [], a tool that uses machine learning (adaptive boosting model implemented in r) to integrate somatic variant calling from multiple tools (mutect, jointsnvmix2, somaticsniper, vardict, and varscan2) from only whole genome or only whole exome platform to identify somatic variants. we applied somaticseq using the default trained model built […]

PMCID: 5636151
PMID: 29020110
DOI: 10.1371/journal.pone.0186175

[…] for haplotypecaller (99.3% sensitivity and 99.9% precision), samtools (99.6% sensitivity and 99.8% precision), and freebayes (98.8% sensitivity and 99.8% precision). atlas2 (72.5% sensitivity), and jointsnvmix (72.0% sensitivity) identified the lowest number of snvs., next, we looked at the concordance of calls between all callers. for the exome data, all ten germline callers correctly […]

PMCID: 5244592
PMID: 28103803
DOI: 10.1186/s12859-016-1451-5

[…] distinguishes true rare variants from the sequencing errors []. however, the bottleneck of crisp is its low computational efficiency due to a calculation of a large number of contingency tables., jointsnvmix introduces two bayesian probabilistic models (jointsnvmix1 and jointsnvmix2) to jointly analyze a tumour-normal paired allelic count of ngs data []. jointsnvmix derives an expectation […]


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JointSNVMix institution(s)
Department of Molecular Oncology, BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada; Canada’s Michael Smith Genome Sciences Centre, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science; Department of Pathology, University of British Columbia, Vancouver, BC, Canada
JointSNVMix funding source(s)
Supported by Canadian Institutes for Health Research (CIHR) grant #202452, the Canadian Breast Cancer Foundation and the Michael Smith Foundation for Health Research.

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