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Variant Annotation API - use cases #226
The question of use cases for the variant annotation API came up on yesterday's call so we thought it would be good to create an issue to share ideas.
As well as the approach discussed - querying for variants and their annotations in a dataset/ annotation set between 2 points on a sequence, we would also interested in using the API to allow the submission of variants for which we do not hold the dataset and returning annotations based on the submitted positions/allele changes and the reference data we hold.
It may also be useful to allow some filtering of the response, such as returning only missense variants.
The use case I am most interested in at this point would allow for the retrival of variants which fall on certain genes. For a simple example, I have a VCF file generated via somatic mutation calling. This VCF now exists as a VariantSet in the database, from which I would like to query at the gene level to satisfy the following two generic uses cases: