dbscSNV example

This example was contributed by Somak Roy. It creates an echtvar zip file from the dbscsnv zip file:

Step 1: Download dbscSNV v1.1 database

download from: https://usf.app.box.com/s/ffwlywsat3q5ijypvunno3rg6steqfs8

filename should be: dbscSNV1.1.zip

Step 2: Convert the zip file to VCF

Download and execute the script dbscsnv.py to convert the zip file to a VCF file containing the ADA and RF scores for hg38 (default)

python dbscsnv.py  dbscSNV1.1.zip | bgzip -c > dbscSNV-1.1.vcf.gz

The script can also be used to pull the hg19 database as well by specifying the --genome hg19 option. The script also gets rid of variants mapped to the random and alternative assembly contigs.

Step 3: Create dbscsnv.json

This file tells echtvar which fields to encode and how to label them. The following contents are a good start:

[
  {
    "field": "ADA_SCORE",
    "alias": "dbscsnv_ADA_SCORE",
    "multiplier": 1000000
  },
  {
    "field": "RF_SCORE",
    "alias": "dbscsnv_RF_SCORE",
    "multiplier": 1000000
  }
]

Step 4: create echtvar archive

This creates dbscsnv_ev.echtvar.zip which can be use by echtvar anno

echtvar encode dbscsnv_ev.echtvar.zip dbscsnv.json dbscSNV-1.1.vcf.gz