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Virmid specifications

Information


Unique identifier OMICS_00095
Name Virmid
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some short reads sequenced from a pure control sample and a potentially mixed disease sample.
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.2.0
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Vineet Baf <>
  • person_outline Sangwoo Kim <>

Publication for Virmid

Virmid citations

 (10)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] 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 corollary […]

library_books

Identification of metastasis driver genes by massive parallel sequencing of successive steps of breast cancer progression

2018
PMCID: 5749725
PMID: 29293529
DOI: 10.1371/journal.pone.0189887

[…] available somatic variant callers: eb call [], mutect [], seurat [], shimmer [], indelocator (http://www.broadinstitute.org/cancer/cga/indelocator), somatic sniper [], strelka [], varscan 2 [] and virmid []. the union of putative somatic mutations, except positions in intronic, intergenic, downstream and non-coding rna intronic areas, reported by the nine somatic variant callers was used […]

library_books

Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants

2017
PMCID: 5731933
PMID: 29254223
DOI: 10.18632/oncotarget.22116

[…] using pre-processing aligned reads separately in tumor and normal samples; strelka [], which reports the most likely genotype for tumor and normal samples based on a bayesian probability model); and virmid []., wes: wes raw data was processed as previously described []. variant calling and annotation were performed with samtools (http://samtools.sourceforge.net 0.1.18) and varscanv211 […]

library_books

Genomic Analyses of Breast Cancer Progression Reveal Distinct Routes of Metastasis Emergence

2017
PMCID: 5343450
PMID: 28276460
DOI: 10.1038/srep43813

[…] using nine publicly available somatic variant callers: eb call, mutect. seurat, shimmer, indelocator (http://www.broadinstitute.org/cancer/cga/indelocator), somatic sniper. strelka, varscan 2 and virmid. all putative somatic mutations reported by at least one somatic variant caller, except positions in intronic, intergenic, downstream and non-coding rna intronic areas, were used to select […]

library_books

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

2016
PMCID: 4803342
PMID: 27002637
DOI: 10.1371/journal.pone.0151664

[…] from five breast cancer patients to evaluate the performance of nine publicly available somatic variant callers: ebcall, mutect, seurat, shimmer, indelocator, somatic sniper, strelka, varscan 2 and virmid for the detection of single nucleotide mutations and small deletions and insertions. we report a large variation in the number of calls from the nine somatic variant callers […]

library_books

Establishment and characterisation of patient derived xenografts as paraclinical models for gastric cancer

2016
PMCID: 4772087
PMID: 26926953
DOI: 10.1038/srep22172

[…] from the mouse reference genomes. then, we removed duplicated reads by using samtools. we called somatic mutations, including single nucleotide variants and small insertions/deletions using virmid and mutect (). to determine the potential functional consequences of detected variants, we annotated them using vep (ensembl’s variant effect predictor). to determine high-confidence variants, […]


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Virmid institution(s)
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA; Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, Rady Children’s Hospital, University of California at San Diego, La Jolla, CA, USA; School of Information and Communications, Gwangju Institute of Science and Technology, Gwangju, Korea; Department of Computer Science, Stony Brook University, NY, USA; Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
Virmid funding source(s)
Supported by the National Science Foundation (NSF-CCF- 1115206), National Institute of Child Health and Human Development (1P01HD070494-01) and National Institute of Health (5R01-HG004962, U54 HL108460).

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