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GermlineFilter specifications


Unique identifier OMICS_22798
Name GermlineFilter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes


No version available


  • person_outline Paul Boutros <>

Publication for GermlineFilter

GermlineFilter citation


Germline contamination and leakage in whole genome somatic single nucleotide variant detection

PMCID: 5793408
PMID: 29385983
DOI: 10.1186/s12859-018-2046-0

[…] with the amount of infiltrating normal cells. the specific germline variants leaked differed by tumour and algorithm. to aid in quantitation and correction of leakage, we created a tool, called germlinefilter, for use in public-facing somatic snv databases., the potential for patient re-identification from leaked germline variants in somatic snv predictions has led to divergent open data […]

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GermlineFilter institution(s)
Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada; Sage Bionetworks, Seattle, WA, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR, USA; Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
GermlineFilter funding source(s)
Supported by the Government of Ontario.

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