Building a variant database (atlas add)

See installation for install instructions

Download pre-made database

📘

mongod

mongod should be running in the background.

Download database of 3449 M. tuberculosis Variant Sets

Download data from https://www.dropbox.com/s/2qms89nb1y5ii1r/atlas-tb-2016-03-18.tar.gz?dl=1

Run:

Shell

tar -zxvf  atlas-tb-2016-03-18.tar.gz
mongorestore atlas-tb-2016-03-18

You can query the database natively from the mongo shell (run mongo) but we recommend you use the python interface.

Or build your own database from VCFs

The variant database is inspired by the (GA4GH schema)[ga4gh.org/#/schemas]. Implementation available (here)[https://github.com/phelimb/ga4gh-mongo]

Shell

usage: atlas add [-h] [--db_name db_name] [-q] [-m METHOD] [-f]
                 vcf reference_set

positional arguments:
  vcf                   a vcf file
  reference_set         reference set

optional arguments:
  -h, --help            show this help message and exit
  --db_name db_name     db_name
  -q, --quiet           do not output warnings to stderr
  -m METHOD, --method METHOD
                        variant caller method (e.g. CORTEX)
  -f, --force           Force recreate VariantSet

To add a VCF to the database db_name run

Shell

atlas add --db_name :db_name sample.vcf :reference_set_name

Use the --method argument to specify the variant caller or pipeline used (if you'll have multiple Call Sets per sample)

Text

atlas add --db_name :db_name --method freebayes sample.vcf :reference_set_name