BAMSurgeon specifications

Unique identifier:
Command line interface
Input data:
An indexed reference genome, a pre-existing file and a list of intervals along with the SV type and parameters.
Biological technology:
Programming languages:
Python, Shell (Bash)
Computer skills:
Software type:
Restrictions to use:
Input format:
Operating system:
MIT License
samtools/wgsim/tabix, pysam, bwa, velvet, exonerate, picard


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BAMSurgeon distribution


BAMSurgeon support



  • Paul┬áBoutros <>
  • Adam Ewing <>


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Ontario Institute for Cancer Research; Toronto, ON, Canada; Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA; Mater Research Institute; University of Queensland; Woolloongabba, QLD, Australia; Computational Biology Program; Oregon Health & Science University; Portland, OR, USA; Sage Bionetworks; Seattle, WA, USA; Department of Bioinformatics and Computational Biology; University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genetics; University of Alabama at Birmingham; Birmingham, AL, USA; Informatics Institute; University of Alabama at Birmingham; Birmingham, AL, USA; IBM Computational Biology Center; T.J.Watson Research Center; Yorktown Heights, NY, USA; Department of Medical Biophysics; University of Toronto; Toronto, ON, Canada; Department of Pharmacology & Toxicology; University of Toronto; Toronto, ON, Canada

Funding source(s)

Supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, Prostate Cancer Canada, the Movember Foundation - Grant #RS2014-, Movember funds through Prostate Cancer, Genome Canada through a Large-Scale Applied Project contract, the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada, and the Canada Foundation for Innovation (CFI), a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award, a CIHR Computational Biology Undergraduate Summer Student Health Research Award, an Australian Research Council Discovery Early Career Researcher Award DE150101117, the Mater Foundation and National Institutes of Health (NIH) grants: R01-CA180778 and U24-CA143858.

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