Commit b5e22242 authored by Daniel Teixeira's avatar Daniel Teixeira
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parents 30a882c5 e7d02d2b
## Current implementation
This beacon queries 20K samples coming from ArrayMap from here:
http://arraymap.org/api/?db=arraymap&qcveto=1&api_out=samples&icdm_m=8,9&api_doctype=jsondata
<img src="/img/current_implementation.jpg" class="img-thumbnail img-responsive">
**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. A mapping 1:1 is done on the fly to convert from GRCh to HG.
* 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.
* matchedSegment: This is DEBUG info.
* NOT_BEACON_totalInDataSet: This is also debug info but could be nice to include it as well on Beacon
**Example**
Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: [query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL](http://beacon-arraymap.vital-it.ch/v0.2/query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL)
Query chromosome 11 at position 34439881 for the dataset 8070/3, showing a deletion: [query?chromosome=11&position=34439881&reference=GRCh38&dataset=8070/3&variantClass=DEL](http://beacon-arraymap.vital-it.ch/v0.2/query?chromosome=11&position=34439881&dataset=8070/3&variantClass=DEL)
**Outcome from the meeting with Jordi (Feb, 10, 2016):**
......@@ -229,4 +233,5 @@ Open questions:
2. assign it the first reference genome's value of the data structure.
3. ask the Beacon team if they can make this optional property.
4. ask the Beacon team if they can replace the property type by a list of strings (instead of a string).
5. clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)
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5. clarify CIPOS and CIEND in VCF v4.2 for DUP/DEL (i.e. CIPOS=-500,500;CIEND=-500,500)
- currently, we belief that this is a range, e.g. +/- 500 for POS and END
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