eagle-i Oregon Health & Science UniversityOregon Health & Science University
See it in Search
This page is a preview of the following resource. Continue onto eagle-i search using the button on the right to see the full record.

Spellman Lab mutation calling pipeline

eagle-i ID


Resource Type

  1. Algorithmic software suite


  1. Resource Description
    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
  2. Contact
    Peto, Myron, Ph.D.
  3. Used by
    Paul Spellman Laboratory
  4. Data Input
    FASTQ files from an Illumina Sequencer
  5. Data Output
    List of variants found
  6. Data Output
    Aligned reads from sequencer (.bam file)
  7. Software purpose
    Sequence comparison objective
  8. Software purpose
    Sequence alignment objective
  9. Website(s)
  10. Related Technique
  11. Developed by
    Peto, Myron, Ph.D.
  12. Coded in
Provenance Metadata About This Resource Record
Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016