GemDb37

MongoDb Variant database for human genome build 37, includes public annotations and various TGen projects.

Access - Download Robo 3T (open source) or your favorite MongoDb GUI port: 25755 server: labdb01.tgen.org

db: markers collection: germline or tumor

Indexes - In Mongo since it is no-sql, it instead uses "indexes" on fields. When you look under the 'tumor' collection there is a folder called 'Indexes'. If you query using the fields that are listed there then your queries will be fast, otherwise they will be slow.

Queries (Quick Reference) - Look up mongodb queries - they are "json" based so they are fairly straightforward, although they can get more complex.

Examples -

For searching on a patient:
{'variants.studyPatient':'mystudy.mypatient'}

For searching on a study:
{'study':'myStudy'}

If a patient has multiple samples:
{'variants.projectRun':'myprojectrun'}

VCF/Annotations -

The VCF file is contained within the "variants" subdocument

For searching a 'biomarker' event or 'variant':
    {'coord':'chr1:1038971:A:C'}

As far as where the annotations/snpeff are (they are in subdocument structure):
    "annotate"    
    "snpeff"

Other important fields : "effect" (contains gene and the mutation/event) "gene" "aberration" subdocument - contains mutation/event info "variants.filter" - PASS, LOWQC determined by GemDb.

tgen/GemDb37

GemDb37