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Paul Spellman Laboratory


The Spellman Lab is interested in using genetic, genomic, and proteomic data to understand and model the biology of cancer and to develop methods to effectively deploy therapeutic agents in the age of molecularly guided medicine.

Members of the lab use a combination of conventional molecular biology, high throughput genomic and proteomic assays, and bioinformatic analyses in their work.





  • Beyond the bam file: Analysis ( Algorithmic software suite )

    An analysis pipeline that includes the following components:
    muTect: Cancer-specific variant calling
    ANNOVAR: Annotate mutation
    Breakdancer? Delly?: Structural variant calling
    OHSU proprietary pipeline: Copy number analysis

  • Spellman Lab mutation calling pipeline ( Algorithmic software suite )

    A GATK-based pipeline for aligning tumor and normal sequencing reads.

    This perl script programmatically preps and pushes data through a processing pipeline that includes the following tools:

    BWA mem + SAM tools: Read alignment
    Picard Tools: Mark duplicates
    GATK (RealingerTargetCreator, IndelRealinger): Local Realignment
    GATK (BaseRecalibration and PrintReads): Re-calibrate quality scores

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Last updated: 2013-11-06T13:34:07.447-06:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016