Commit af225b8a authored by Daniel Teixeira's avatar Daniel Teixeira
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parents 5ca11ec8 0ba4a286
......@@ -4,7 +4,7 @@
**Comments**
* reference genome: In [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the values expected for human data is of GRCh? format, whereas arrayMap uses hg?? nomenclature.
* reference genome: In [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the values expected for human data is of GRCh? format, whereas arrayMap uses HG nomenclature.
* allele: [In Beacon 0.2 specifications](https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit), the parameter is required. However, it does not make sense at all for arrayMap (in which no sequence related data exists).
* variantClass: This is a new parameter. The value equals DUP corresponds to SEGTYPE=1 (gain) in arrayMap, while DEL is for SEGTYPE=-1 (loss). The parameter is mandatory.
* sampleuid: This is DEBUG info.
......@@ -17,7 +17,7 @@ Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a delet
**Outcome from the meeting with Jordi (Feb, 10, 2016):**
It chould be ok to have the variantClass in Beacon v0.3. As for ranges, this is more complicated and requires lots of discussions. We will probably go in 2 steps:
It should be ok to have the variantClass in Beacon v0.3. As for ranges, this is more complicated and requires lots of discussions. We will probably go in 2 steps:
* add P (duPlication) to the list of allowed values for the allele parameter.
* modify I (insertion) slightly by making the "sequence" string optional, i.e. be fuzzy about what was inserted.
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