multiSNV statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left SNV detection chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

Documentation


Maintainer


  • person_outline Malvina Josephidou <>

Publication for multiSNV

multiSNV in publications

 (4)
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 […]

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 […]

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 […]

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, […]


To access a full list of publications, you will need to upgrade to our premium service.

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

multiSNV reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review multiSNV