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ga4gh / ga4gh-schemas

Models and APIs for Genomic data. RETIRED 2018-01-24
http://ga4gh.org
Apache License 2.0
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Call schema not suited for variant calls with no coverage #727

Closed wdesouza closed 7 years ago

wdesouza commented 7 years ago

As recommended by @dcolligan, I am adding this issue here to describe a problem that I found on GA4GH schemas and was first described at ga4gh/server#1389.

When the VCF file has variant calls with no coverage represented by ./. the GA4H API server cannot convert this data to the appropriated value. The solution I found was change this line to:

google.protobuf.ListValue genotype = 3;

After compiled protobuf files and updated the server it worked fine.

mbaudis commented 7 years ago

+1

... or more. Anonymous positions are necessary for structural variants, which frequently are imprecise and frequently have no utility for providing the reference base.

kozbo commented 7 years ago

@david4096 any reason to wait on a PR to close this out?

mbaudis commented 7 years ago

@kozbo @david4096 This is handled by https://github.com/ga4gh/schemas/pull/735/files#diff-70572e12d3d541d3f4fbdd23c76ebb64 . I've just added some more doc there. Should be merged ASAP...