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Protocols

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

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No version available

Documentation


Maintainer


  • person_outline Sohrab Shah

Publication for mutationSeq

mutationSeq citations

 (7)
call_split

Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice

2018
PLoS One
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434
call_split See protocol

[…] ing 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 from the resu […]

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

[…] ment 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 classifi […]

library_books

Detection and genomic characterization of a mammary like adenocarcinoma

2017
PMCID: 5701302
PMID: 28877932
DOI: 10.1101/mcs.a002170

[…] oBloom 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 was […]

library_books

Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma

2017
PMCID: 5593158
PMID: 28514723
DOI: 10.1101/mcs.a001628

[…] at 42% tumor content, which is a lower tumor content than estimated via pathology review and assessment (72.5%).A combination of tools was used to perform somatic SNV calling: SAMtools (v0.1.17) (), MutationSeq (v1.0.2) (), and Strelka (v1.0.6) (); small insertions and deletions were identified using Strelka (v1.0.6) () and Trans-ABySS (v1.4.10) (; ). Small-mutation (SNV, indel) calling takes int […]

library_books

Molecular etiology of an indolent lymphoproliferative disorder determined by whole genome sequencing

2016
PMCID: 4849852
PMID: 27148583
DOI: 10.1101/mcs.a000679

[…] 0.1.1, using the “K18 params Illumina stromalRatio Hyper10k min10max200” parameter matrix, downloaded from http://compbio.bccrc.ca/software/apolloh/) (), single-nucleotide variants (SAMtools v0.1.17, MutationSeq v1.0.2 [], Strelka v0.4.6.2 []), and small insertions and deletions (Strelka v0.4.6.2). RNA-seq reads were analyzed with JAGuaR (Junction Alignments to Genome for RNA-Seq Reads; ) to inclu […]

library_books

Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing

2014
Cancer Inform
PMCID: 4179624
PMID: 25288881
DOI: 10.4137/CIN.S13779

[…] both samples using joint diploid genotype likelihoods or shared allele frequency between the samples. A number of somatic mutation tools have emerged in the past 2 years, including deepSNV, Strelka, MutationSeq, MutTect, QuadGT (http://www.iro.umontreal.ca/~csuros/quadgt), Seurat, Shimmer and SolSNP (http://source-forge.net/projects/solsnp), jointSNVMix, SomaticSniper, VarScan2, and Virmid. Each […]

Citations

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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.

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