#+title: Validated low frequency somatic variants and copy number heterogeneity with bcbio
#+author: Brad Chapman \newline Bioinformatics Core, Harvard Chan School \newline https://bcb.io \newline http://j.mp/bcbiolinks
#+date: 9 April 2018

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* Talk

** Interoperable, community built workflows

#+ATTR_LATEX: :width 1.0\textwidth
[[./images3/bcbio_nextgen_highlevel.png]]

\vspace{1cm}
https://github.com/bcbio/bcbio-nextgen

** Validation

\Large
- Common Workflow Language (CWL) descriptions
- Multiple platforms (HPC, DNAnexus, Arvados, SevenBridges)
- Multiple analysis areas:
   - \Large Germline calling; single and joint
   - \Large Somatic low frequency
   - \Large Structural variants

\small
https://github.com/bcbio/bcbio_validation_workflows

** Somatic low frequency variants

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[[./images12/grading-summary-gm1.png]]

\vspace{0.1cm}
\large DeepVariant \scriptsize (https://github.com/google/deepvariant)

\vspace{0.2cm}
https://github.com/bcbio/bcbio_validations/tree/master/strelka2

** Tumor heterogeneity

\Large
- Difficult inputs: ctDNA, tumor-only, FFPE, panels
- Baseline calls, variants + CNVs with CNVkit
- Mixture of methods
  - \large TitanCNA -- tumor/normal; purity + subclonal CNVs
  - \large ichorCNA -- circulating tumor; purity estimation
  - \large PureCN -- tumor only; purity + subclonal CNVs
  - \large PhyloWGS -- evolutionary influence from subclonal
- Need standard validation sets
