#+title: Quantifiable and scalable detection of genomic variants
#+author: Brad Chapman
#+creator: Bioinformatics Core, Harvard School of Public Health
#+date: 26 June 2013

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*   

[[../bosc2013_bcbio_nextgen/images/bcbio_nextgen_highlevel.png]]

* Development goals

- Quantifiable: assess variant quality
- Scalable: 1500 whole genome samples
- Reproducible: text-configurable, provenance, version tracking
- Community developed: open source, documented and widely deployable

* Quantify quality

[[https://raw.github.com/chapmanb/bcbb/master/posts/calling_pipeline_compare/grading-summary-prep-callerdiff.png]]

Reference materials: [[http://www.genomeinabottle.org/]]

* Parallel scaling

[[https://raw.github.com/chapmanb/bcbio-nextgen/master/docs/contents/images/parallel-clustertypes.png]]

Infrastructure: [[http://ipython.org/ipython-doc/dev/parallel/index.html]]

* Reproducible configuration

#+BEGIN_SRC yaml
  - files: [NA12878-NGv3-LAB1360-A_1.fastq.gz, NA12878-NGv3-LAB1360-A_2.fastq.gz]
    description: NA12878
    analysis: variant2
    genome_build: GRCh37
    algorithm:
      aligner: bwa
      recalibrate: gatk
      realign: gatk
      variantcaller: [gatk, freebayes, gatk-haplotype]
      coverage_interval: exome
      coverage_depth: high
      platform: illumina
      quality_format: Standard
      validate: NA12878-nist-v2_13-NGv3-pass.vcf
#+END_SRC

* Community developed

- Fully automated installation: CloudBioLinux
- Deployable on multiple clusters (LSF, SGE, Torque)
- Integrated with web platforms (Galaxy, STORMSeq)
- Open source and documented

[[https://github.com/chapmanb/bcbio-nextgen]]

#+BEGIN_SRC emacs-lisp :exports results :results silent
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  "<h2>%t</h2>
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   <h4><a href='https://github.com/chapmanb'>@chapmanb</a></h4>
   <h4>%d</h4>")
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