Michael Baudis

These are the current examples we use for [Beacon+](http://beacon.progenetix.org). It would be nice to have them reviewed/fixed (we have a custom back end). #### Standard precise Beacon variant query ```...

Markdown from YAML?! We generate the whole set of SchemaBlocks examples and .md ... from the YAML file through a simple Perl script. E.g. * https://github.com/ga4gh-schemablocks/blocks/blob/master/src/yaml/variant.yaml leads to * https://schemablocks.org/schemas/blocks/Variant.html...

@sdelatorrep Is there a planned transition to JSON Schema? Since we'll do the same for SchemaBlocks (documentation from schema using some "standard tooling" - ask @relequestal... - && doc for...

You need mateName=chro... + variantType=BND to specify a fusion event with known partners. Sent from my iPad > On Apr 24, 2019, at 9:00 AM, Stefan Negru wrote: > >...

@blankdots You’re correct; but IMO a well-formed fusion query should specify BND, even if it is implicit. I’m not sure how to go further about this - specification or documentation...

@teemukataja In the current proposal, `mateName` would be a specification for the `end` position. A `BND` with a specified `mateName` would correspond to a translocation if on different chromosome. ```...

@teemukataja SAee the example above, corresponding to an imprecise fusion event (e.g. a MYC-IGL translocation, variant Burkitt lymphoma). A precise query (which doesnt make much sense, since breakpoints are rarely...

@teemukataja For `BND` variant queries w/o a `mateName`, all types of variants representing a structural sequence disruption could be queried. In our Beacon+ instance, we just match e.g. on the...

This is great! We'll (all) should comb through & then move tis, also, to the Beacon website. To be clarified e.g.: * "Total number of samples in the dataset" ......

@teemukataja The statement sampleCount Total number of samples in the dataset Number of test subjects (people) in the dataset is misleading. A dataset in the "variant dataset" sense is a...