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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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Versioning


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Documentation


Maintainers


  • person_outline Vineet Baf
  • person_outline Sangwoo Kim

Publication for Virmid

Virmid citations

 (11)
library_books

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

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] lable, 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 of th […]

library_books

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

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

[…] ly 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 to sel […]

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
Oncotarget
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 (http://dkobo […]

library_books

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

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

[…] med 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 chro […]

library_books

Clonal Evolutionary Analysis during HER2 Blockade in HER2 Positive Inflammatory Breast Cancer: A Phase II Open Label Clinical Trial of Afatinib +/ Vinorelbine

2016
PLoS Med
PMCID: 5140058
PMID: 27923043
DOI: 10.1371/journal.pmed.1002136

[…] Picard (v1.54), and indel realignment performed with GATK IndelRealigner (v1.0.6076) []. Somatic single nucleotide variant (SNV) calling was performed using VarScan2 (v2.3.7) [], MuTect (v1.1.7) [], Virmid (v1.1.0) [], and Strelka (v1.0.14) []. SNVs called by ≥2 tools were further filtered for variant allele frequency (VAF) ≥5%. Small indels were identified using Pindel (v0.2.5a7) [] and VarScan2 […]

library_books

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

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

[…] ons, while other of the studied variant callers report more divergent sets of positions. Sequencing depth had markedly diverse impact on individual callers. For SNV calling, we report EBCall, Mutect, Virmid and Strelka to be the most reliable somatic variant callers for both medium and high coverage sequencing data. Strelka is, however, a very conservative somatic variant caller. For indel calling […]

Citations

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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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