Questions about GA4GH Beacons

Question

[Pierre Lindenbaum]

There are so many things to read about ga4gh: I'm a little bit lost. So here are a few questions about GA4GH / Beacons :

• I've got some VCF files. What is the correct way to expose my data? How can I secure my data for my collaborators? Is there a java server implementation?
• If I build a beacon server from scratch (learning... learning...) is there a tool that can be used to test if my implementation is ga4gh compliant?
• Where should I declare that I'm providing a beacon server?
• The schema use avro; Is it possible to return plain JSON or does using Avro means that I need to serialize the data as a binary stream? Is there any API converting jaav+htsjdk to avro?
• What's the best place to ask questions about ga4gh?

Answer 1

[skeenan]

I've got some VCFs file: what is the correct way to expose my data? how can I secure my data for my collaborators? Is there a java server implementation?

There are a number of servers to get you started - see developers tab on http://ga4gh.org/#/beacon

If I build a beacon server from scratch (learning... learning...) is there a tool that can be used to test if my implentation is ga4gh compliant?

There is a suite of compliance tests for GA4GH schemas, at the moment coverage has not extended to Beacons, yet. However the schema is very simple (as it was intended to be) and it would not be difficult to confirm compliance.

where should I declare that I'm providing a beacon server?

http://beacon-network.org

the schema use avro (https://avro.apache.org/); Is it possible to return plain JSON or does using Avro means that I need to serialize the data as a binary stream? is there any API converting jaav+htsjdk to avro?

It is not necessary to use AVRO to serve your Beacon results. Plain old JSON which is conferment to the schema is acceptable.

what's the best place to ask questions about ga4gh?

• https://github.com/ga4gh/schemas/issues
• https://github.com/ga4gh/beacon-team/issues

Answer 2

[Maximilian Haeussler]

This should be the easiest beacon server to run (disclosure: I'm the developer): https://github.com/maximilianh/ucscBeacon

Should run on any OS, brings its own webserver or runs as a CGI. Can import directly: VCF, Complete Genomics, BED, HGMD and LOVD formats. A single python script, no dependencies. Let me know if something doesn't work for you.

Answer 3

[Sean Davis]

These sites are actually pretty useful for general ga4gh issues.

• http://ga4gh.org/
• https://github.com/ga4gh

For beacons:

• http://ga4gh.org/#/beacon
• https://github.com/Genecloud/simplebeacon