#+title: Building a community menagerie of automated variant validations
#+author: Brad Chapman \newline Bioinformatics Core, Harvard Chan School \newline http://j.mp/bcbiolinks
#+date: 27 June 2018

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* Validation

** You have a variant calling pipeline

#+ATTR_LATEX: :width 0.5\textwidth
[[./images/cwl-variant.png]]

https://github.com/bcbio/bcbio-nextgen

** Is it good? How good? What data types?

[[./images/grading-summary-gj1.png]]

\scriptsize
https://github.com/bcbio/bcbio_validations/tree/master/gatk4

** Does it work on my difficult samples?

\Large
Somatic tumor-only FFPE

[[./images/grading-summary-ras.png]]

\scriptsize
https://github.com/bcbio/bcbio_validations/tree/master/somatic-lowfreq

** Can I use it to improve callers?

[[./images/grading-summary-dv.png]]

\scriptsize
https://github.com/bcbio/bcbio_validations/tree/master/deepvariant

** Will it run correctly on my platform?

\Large
- Local machines and HPC: Cromwell, Toil
- AWS, GCP, Azure
- Arvados
- DNAnexus
- SevenBridges

\normalsize
http://bcbio-nextgen.readthedocs.io/en/latest/contents/cwl.html

** Automated validations for everything

\LARGE
- Workflows

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

\LARGE
- Analyses

\normalsize
https://github.com/bcbio/bcbio_validations

\LARGE
- Join the community: GiaB, GA4GH, NIH Data Commons

\normalsize
https://github.com/bcbio/bcbio-nextgen
