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BaderLab / GenomeClinic-PGX

Web application for clinical pharmacogenomic interpretation
GNU Lesser General Public License v3.0
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local monogDB server to store annotated variants #5

Closed patmagee closed 9 years ago

patmagee commented 9 years ago

In order to begin production of for the pharmacogenomics app as well as the discovery app we need to run a local instance of a mongoDB that can store annotated variant information in a queryable manner. The database should have individual tables for projects that contain a foreign key to point to a patient table. Each patient will receive a separate table to store their variants. Multiple projects can point to the same patient.

Specific points of this are:

  1. Create a module to store variants within a mongoDB
  2. Annotate using annovar with the following annotations: a. ljb26_all b. cg69 c. esp65000_all d. 1000G2014-sep e. CGD f. clinvar
  3. Extract all annotations
  4. Store Annotations
  5. Write functions to enable easy query ability for annotated variants.
patmagee commented 9 years ago

I have implemented the local storage of vcf files in a mongoDB after annotation.

Objectives 1-4 are complete.

Objectives left: 5

ronammar commented 9 years ago

This is basically done and implemented.

keypanqi commented 7 years ago

Hi,patmagee ~ I cannot download some annotation database(ljb26_all and 1000G2014-sep) with the command perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ljb26_all annovar_db/ . Could you tell me ,why couldn't I and how did you download them~ I will appreciate ,if you can send these files (ljb26_all and 1000G2014-sep) to me. Here is ,my email: 1053095150@qq.com.