WARNING: Not actively maintained!
Given a particular set of variants for an individual or a cohort, the code here will allow you to interactively annotate the sequence variants using annotation resources available in BigQuery. Note that if there is a newer version of the annotation resource that you wish to use, you can load it into BigQuery.
There is only one example here at the moment but see also similar work:
- http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/COSMIC.html
- https://github.com/googlegenomics/bigquery-examples/tree/master/platinumGenomes
- http://googlegenomics.readthedocs.io/en/latest/use_cases/annotate_variants/interval_joins.html
TODO: add more example queries, Datalab notebooks and RMarkdown.
Datalab Notebook Examples
- Notebook InteractiveVariantAnnotation.ipynb will return variants for sample NA12878 that are:
- annotated as 'pathogenic' or 'other' in ClinVar
- with observed population frequency less than 5%