SomaticSeq statistics

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Citations per year

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Popular tool citations

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Tool usage distribution map

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Associated diseases

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SomaticSeq specifications

Information


Unique identifier OMICS_10002
Name SomaticSeq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
regex, R, GATK, snpEFF, snpSIFT, dbSNP, COSMIC
Maintained Yes

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Maintainer


  • person_outline Hugo Y.K. Lam <>

Publication for SomaticSeq

SomaticSeq in publications

 (2)
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] 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 classifiers (random […]

PMCID: 5657037
DOI: 10.1186/s12864-017-4134-3

[…] from multiple somatic variant callers improve the identification of somatic variants over individual callers. for example, kim et al. developed a statistical model that combines multiple callers []. somaticseq [] uses adaptive boosting model and cake [] uses majority voting to classify a variant as somatic. it is worth noting is that the aforementioned ensemble approaches have all been developed […]


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SomaticSeq institution(s)
Bina Technologies, Chinahe Sequencing, Redwood City, CA, USA

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