OncoKB for GatewaySeq

Resources

https://github.com/dhslab/cle-gatewayseq

https://www.oncokb.org/swagger-ui/index.html

Configuration

See template in

config/gatewayseq_config.template.json

Add the OncoKB API key here

"oncokb_api_key": "ADD API KEY HERE",

This file also configures the tumor types to download from OncoKB and the API timeout in seconds

Usage

Read in CONFIG and GatewaySeq JSON file and add OncoKB annotation under .REPORTING.oncokb, with JSON output to STDOUT

# Production use
py/oncokb_annotate_json.py CONFIG JSON

# Include variant information in each oncokb entry for debugging
py/oncokb_annotate_json.py --include-variant CONFIG JSON

Output

The script adds a section to the top-level REPORTING object, creating it if needed

"REPORTING": {
  "oncokb": { ... }
}

There are two sections under oncokb

"oncokb": {
  "PASS": [ ... ],
  "Filtered": [ ... ]
}

corresponding to the top-level VARIANTS section in the input JSON file

"VARIANTS": {
  "PASS": [ ... ],
  "Filtered": [ ... ]
}

Elements in the oncokb section arrays correspond to elements in the VARIANTS arrays, with one object per VARIANTS element as follows

{
  // The first API call made is a preflight check with no tumor type 
  // specified to see if OncoKB has any data for the variant
  
  // Only if --include-variant was used
  "variant": [ ...variant information... ],

  "apiStatus": "low_vaf|api_failed|not_found|ok"

  "apiStatus": "low_vaf"
  // The variant is from the Filtered section
  // with VAF below specified minimum (default 1.0%) and is not queried
  // further

  "apiStatus": "api_failed"
  // Additional debugging data will
  // be stored  under "apiRequests", which can be either an exception
  // or HTTP status information

  // An exception occurs if the network is down or the API is
  // otherwise unreachable or unresponsive
  "apiRequests": { "exception": "exception string" }

  // OR if the server responded, but the status returned was not ok, 
  // eg the API page was not found, a bad request was made, 
  // the call timed out (timeout is set to 60s),
  // or an internal server error occurred
  "apiRequests": { 
    "status_code": "HTTP status code", 
    "reason": "HTTP status reason"
  }

  "apiStatus": "not_found"
  // The API call succeeded but OncoKB has
  // no data for the variant, and no further queries for the variant 
  // are made

  "apiStatus": "ok"
  // The variant has data in OncoKB, and a new API
  // call is made for each tumor type, with data stored under a key
  // named with that tumor type containing an object
  // The object contains "apiStatus"/"apiRequests" keys
  // as in the preflight check (in case the preflight is "ok" but a 
  // tumor type call is "not_found" or "api_failed", which should not 
  // normally happen) as well as the OncoKB data (if tumor type "apiStatus" 
  // is "ok"), eg
  "Thyroid": {
    "apiStatus": "ok",
    // ...OncoKB data...
  }
}      

Docker

Code to build a Docker image based on

registry.gsc.wustl.edu/mgi-cle/myeloseqhd:v2

is under docker/. The Dockerfile is dead simple, just installing the Python requests package

cd docker

# Pull registry.gsc.wustl.edu/mgi-cle/myeloseqhd:v2
# I got errors trying to do a FROM directly, but 
# it works if it is present as a locally pulled Docker image
make pull

# Build the Docker image
make build

# Launch an interactive session for testing, with ../ being
# mounted as /host
make interact