deepSNV specifications

Information


Unique identifier OMICS_02239
Name deepSNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.27.2
Stability Stable
Requirements
methods, RColorBrewer, parallel, graphics, IRanges, GenomicRanges, Biostrings, SummarizedExperiment, rmarkdown, knitr, R(>=2.13.0), VGAM, Rhtslib, VariantAnnotation(>=1.13.44)
Maintained Yes

Subtool


  • Shearwater

Versioning


Add your version

Documentation


Maintainer


  • person_outline Moritz Gerstung <>

Publications for deepSNV

deepSNV in publications

 (16)
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] abandon the diploidy assumption and model joint allele frequencies (ft,fn) instead of joint genotypes (gt,gn). the allele frequency analysis approach is taken by strelka, mutect, lofreq, ebcall, deepsnv, lolopicker, and muse , , , , , , . strelka's core algorithm consists of two steps. first, the posterior probabilities of vafs in tumor and normal, noted as p(ft,fn|dt,dn), are estimated […]

PMCID: 5799254
PMID: 29402884
DOI: 10.1038/s41467-017-02349-8

[…] of the spectra of single-nucleotide variants, ngs reads were aligned to the reference gene. nucleotide occurrence frequencies were then determined in r on the aligned ngs reads using the deepsnv bioconductor package. sequences containing sgrna/crrnas from the pooled lentiviral screens were trimmed from adapter sequences. individual sgrna/crrna sequencing reads were then counted […]

PMCID: 5933925
PMID: 29683424
DOI: 10.7554/eLife.35962.036

[…] figure 1—figure supplement 4. , we identified intrahost single nucleotide variants (isnv) using our empirically validated analysis pipeline (). our approach relies heavily on the variant caller deepsnv, which uses a clonal plasmid control to distinguish between true isnv and errors introduced during sample preparation and/or sequencing (). given the diversity of influenza viruses […]

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

[…] callers called between 36.3% and 55.2% of the snvs, and all tools together called 58.0%. this effect was less pronounced for precision, with almost negligible differences in precision for strelka, deepsnv, shimmer and mutect at different admixture levels. in all, mutect showed the best overall performance for paired tumor-control exome data at all admixture levels, closely followed by strelka […]

PMCID: 5628936
PMID: 28945760
DOI: 10.1371/journal.pgen.1007001

[…] were used when the gistic algorithm was applied., the number of reads for each nucleotide base at each probe position on the affymetrix snp6.0 na32 hg19 annotation was extracted from sequence using deepsnv []. the logarithm of the ratio (logr) between allele a and b and the b allele frequency (baf) were calculated as follows: logri=log2(ai+bi) baf=bi(ai+bi) where ai is the read count for allele […]


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deepSNV institution(s)
Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK; Department of Haematology, Addenbrooke's Hospital, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK
deepSNV funding source(s)
Supported by a Specialized Center of Research grant from the Leukemia Lymphoma Society (LLS), the Kay Kendall Leukaemia Fund, the Wellcome Trust (grant reference 077012/Z/05/Z) and a Wellcome Trust Senior Clinical Research Fellowship (grant reference WT088340MA).

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