live query API does not work for some ClinVar RCVs about myvariant.info HOT 5 CLOSED

Hi,
Thanks for pointing that out!
In Clinvar, RCV000008604, RCV000008605, RCV000008606 and RCV000008607 represents 4 different items. However, these 4 items indeed refer to the same hgvs_id. That's why when loading into our database(we use hgvs_id to index), only one item was included. We will update our parser to deal with this issue (merging duplicate RCV accession numbers). Will keep u updated!

from myvariant.info.

Hi Liu,
In the new release of MyVariant.info, we have fixed this issue. Right now, all items from 'clinvar' with the same hgvs_id but different RCV numbers are merged together. Thus, Multiple RCV ids corresponding to the same hgvs_Id will be grouped in a list under 'rcv_accession' attribute of the same doc.

from myvariant.info.

Thanks for let me know the improvement. Unfortunately, there are still some RCVs missing. For instance, RCV000000019, RCV000117222 and RCV000178096 can not be found in the API. They share the same variant (ClinVar variation ID 9) with other 6 RCVs (RCV000000020, ..., RCV000000025). Is full version of ClilnVar data imported in your db?

from myvariant.info.

Hi Liu,

Thanks for pointing that out! It is indeed a bug in our clinvar_xml parser. It will be fixed in our new data release!

from myvariant.info.

Hi Liu, another new release of MyVariant.info has just came out. In this release, we have fixed this RCV missing issue which u pointed out earlier. In this new release, RCV accession numbers is nested under 'clinvar.rcv' field. If a variant includes multiple rcv records, each record will be represented as an element in a list under "clinvar.rcv" field.
We also have prepared a Jupyter Notebook tutorial demonstrating how to access ClinVar data from MyVariant.info services.
Thanks very much for ur feedbacks. And feel free to contact us if u have any more questions. Thanks!

from myvariant.info.