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I have several questions regarding the ri, as my queries don't behave as I would expect them to.
Is there a way in beacon2-ri to specify the reference sequence name as specified in the beacon specifications. My queries on g_variations work unless I specify the "referenceName"
Are there any limitations on the number of variations the beacon2-ri-tools or ri-api can load? I have 70M variant positions in my dataset, all my 70M positions have an alternate allele in at least one biosample. Once converted to bff using ri-tools, i am left with only 10M variants. I am using the v1 of ri-tools because I cannot make ri-tools-v2 work.
Finally, my last question: is there a way in beacon to query for individuals or biosamples that have several specified variations. So, not specifying one single position or one single range for variations, but two or more. For example, with several queries:
Hi @albodrug ,
thanks for reporting this. Let's go with the questions:
In beacon2-ri-api, you can specify the referenceName as the specifications, with two possible ways of doing it: g_variants?referenceName=22
or g_variants?referenceName=NC_000022.11
In any case, you need to have the identifiers.genomicHGVSId correctly filled in.
I didn't understand what exactly is your issue, but beacon ri tools v2 doesn't have any limit on the number of variants to transform neither does the API in the number of variants you can load. If the issue is with tools v1, we are not mantaining that software anymore (at least in EGA). If you tell me why you can't make tools v2 work I can help you (start an issue there).
In the specifications, right now, this is not possible. There are range queries or bracket queries, but if you want two specific range queries or bracket queries at the same time, you will have to do them one by one. Once said that, in beacon2 RI API I have this implemented (out of the spec) by sending an array of request parameters, like this: curl \ -H 'Content-Type: application/json' \ -X POST \ -d '{ "meta": { "apiVersion": "2.0" }, "query": { "requestParameters": [{ "alternateBases": "G" , "referenceBases": "A" , "start": [ 16050074 ], "end": [ 16050568 ], "variantType": "SNP"},{ "alternateBases": "G" , "referenceBases": "A" , "start": [ 50074 ], "end": [ 150568 ], "variantType": "SNP"}], "includeResultsetResponses": "HIT", "pagination": { "skip": 0, "limit": 10 }, "testMode": false, "requestedGranularity": "record" } }' \ http://localhost:5050/api/individuals
Hello,
I have several questions regarding the ri, as my queries don't behave as I would expect them to.
Finds no variation with referenceName specified
Finds 6 variations, only difference is no referenceName specified. Variations are in different chromosomes.
Are there any limitations on the number of variations the beacon2-ri-tools or ri-api can load? I have 70M variant positions in my dataset, all my 70M positions have an alternate allele in at least one biosample. Once converted to bff using ri-tools, i am left with only 10M variants. I am using the v1 of ri-tools because I cannot make ri-tools-v2 work.
Finally, my last question: is there a way in beacon to query for individuals or biosamples that have several specified variations. So, not specifying one single position or one single range for variations, but two or more. For example, with several queries:
Thanks for any insights or tips!
Have a nice day,
Alex
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