mutationSeq 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

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

mutationSeq specifications

Information


Unique identifier OMICS_00086
Name mutationSeq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
Computer skills Advanced
Stability Stable
Requirements
numpy, scipy, matplotlib, scikit-learn, intervaltree
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Sohrab Shah <>

Publication for mutationSeq

mutationSeq in pipelines

 (2)
2018
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] bwa [] and results filtered to remove all aligned reads with four or more mismatching bases or six or more soft clipped bases. single nucleotide variants (snv) were identified and annotated using mutationseq v4.3.8 [] in paired deep mode with criteria -v -q 30—coverage 100 -t 0.5. the complete list of snvs for all patient groups, is included in . reported snvs were then extracted […]

2017
PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] for each sample. the protocol used for amplicon library construction and singleplex pcr sequencing is the same as in., deep targeted sequences were aligned using bwa and snvs were called using mutationseq in both experiments., copy number information for experiment 2 was obtained from oncosnp-seq analysis of the dah55 and dah56 cell line copy number array measurements (snp6)., in order […]


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

mutationSeq in publications

 (11)
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] bwa [] and results filtered to remove all aligned reads with four or more mismatching bases or six or more soft clipped bases. single nucleotide variants (snv) were identified and annotated using mutationseq v4.3.8 [] in paired deep mode with criteria -v -q 30—coverage 100 -t 0.5. the complete list of snvs for all patient groups, is included in . reported snvs were then extracted […]

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

[…] information is discarded and reads are assembled and re-aligned., machine learning methods have been very successful in classification, and variant calling is essentially a classification problem. mutationseq, somaticseq, snooper, and baysic , , , are representative variant callers that apply machine learning methods. mutationseq extracts relevant features on each site and trains four […]

PMCID: 5701302
PMID: 28877932
DOI: 10.1101/mcs.a002170

[…] tools (bbt) (). wgs variants identified using samtools v0.1.7 mpileup (). the tumor and normal samples were compared with identify somatic events. snvs were called using strelka v0.4.62 () and mutationseq v1.0.2 (). strelka v0.4.62 was also used to called small insertions and deletions. the somatic variant annotation was done with the ensemble database (v69), and the effect calculation […]

PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] sample volumes were mixed and re-suspended with te buffer to obtain the required volume for qpcr., exome sequences were aligned using bwa and snvs were called using samtools in experiment 1 and mutationseq in experiment 2., the 2-step pcr sequencing method used primers that were designed as singleplex primers. chosen target positions were entered into primer3, an online program used […]

PMCID: 5437943
PMID: 28327945
DOI: 10.1093/gigascience/gix015

[…] somatic snvs. the ensembl_vcf tool receives the output of variant callers and selects variants detected by a user-specified number of tools. this example workflow runs four variant callers (strelka, mutationseq, radia and somaticsniper) and runs vcf2maf to annotate the resulting list of variants with support from a sufficient number of tools., additional file fig. s2 achieving parallelization […]


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

mutationSeq institution(s)
Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada; Department of Computer Science, University of British Columbia, Vancouver, BC, Canada; Canada’s Michael Smith Genome Science Centre, University of British Columbia, Vancouver, BC, Canada; Department of Pathology, University of British Columbia, Vancouver, BC, Canada
mutationSeq funding source(s)
Supported by a Canadian Institutes for Health Research (CIHR) Catalyst Grant: Bioinformatics Approaches to Cancer Research, application #202452, the Canadian Breast Cancer Foundation, the Michael Smith Foundation for Health Research and by the OvCaRe - Clear Cell Project.

mutationSeq reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review mutationSeq