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molgenis / data-transform-vkgl

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Variant formatter uses transcript db older than db used by labs #26

Open dennishendriksen opened 4 years ago

dennishendriksen commented 4 years ago

https://github.com/molgenis/data-transform-vkgl/blob/e14e871174413031d9044d8b11bc6884fedd64dd/docker/docker-compose.yml#L18

Alissa Interpret, used by multiple VKGL labs uses RefSeq 2019-11-01 (GCF_000001405.25_GRCh37.p13_genomic.gff) so it possible that variants are reported with transcripts that do not exist in the RefSeq transcript set used in uta_20171026.

More recent databases (either ncbi or uta) are available: http://dl.biocommons.org/uta/