## Quantifiable and scalable detection of genomic variants

#### Brad Chapman

#### Bioinformatics Core, Harvard School of Public Health

#### @chapmanb

#### 26 June 2013

##

## 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

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

## Parallel scaling

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

## Reproducible configuration

    - 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

## 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