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multiSNV specifications

Information


Unique identifier OMICS_07650
Name multiSNV
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Pileup
Output format VCF
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
R::Rcpp, Rinside, inline, Git, cmake, Boost
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Malvina Josephidou

Publication for multiSNV

multiSNV citations

 (4)
library_books

Multi region and single cell sequencing reveal variable genomic heterogeneity in rectal cancer

2017
BMC Cancer
PMCID: 5701298
PMID: 29169336
DOI: 10.1186/s12885-017-3777-4

[…] (hg19, uscc) with the burrows-wheeler aligner []. the aligned bam files were sorted and merged with samtools 0.1.19 []. first, we applied two software, the genome analysis toolkit (gatk 1.6) [] and multisnv [], to identify mutations in multi-region wes. the indels and snvs were identified with gatk 1.6 [] based on dbsnp 135 (www.ncbi.nlm.nih.gov/projects/snp/), and the duplicates were removed […]

library_books

Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi region whole exome sequencing

2017
Nat Commun
PMCID: 5595870
PMID: 28900112
DOI: 10.1038/s41467-017-00650-0

[…] (gatk2.1-8). for mutation calling, we first used the gatk unified genotyper in multi-sample mode to call single nucleotide variations (snvs) and indels. then we applied another joint-calling method multisnv for snv calling and variants qualified in both methods were reserved. indels called by the gatk unified genotyper were manually checked to ensure the fidelity. all variants were annotated […]

library_books

Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia

2017
Nat Commun
PMCID: 5357854
PMID: 28303898
DOI: 10.1038/ncomms14756

[…] of base qualities. samtools mpileup command was used to create pileup files for variant calling. snv and indel detection was performed with gatk, varscan (version 2.3.8), mutect (version 1.1.7) and multisnv. mutations were annotated for read depth of reference and alternate alleles, and ensembl variant effect predictor (version 80) and cosmic (version 72) were used to explore the impact […]

library_books

Evolution of oesophageal adenocarcinoma from metaplastic columnar epithelium without goblet cells in Barrett's oesophagus

2015
PMCID: 4893117
PMID: 26701877
DOI: 10.1136/gutjnl-2015-310748

[…] exome capture libraries were sequenced on an ilumina hiseq. sequencing reads were aligned using bwa and further processed according to the gatk best practices pipeline. mutations were called using multisnv and phylogenetic tree reconstruction was carried out using the maximum parsimony mode of the mega software. due to allelic amplification biases introduced by the repli-g wga step, […]


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multiSNV institution(s)
Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK

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