After generating all VCF files you want to include in the panel, you can use bcftools-merge to merge them into a single Panel of Normal VCF.

Usage

# Enter the Choppy work environment
open-choppy-env
# APP `bcftools-merge` should be installed for the first time
choppy install YaqingLiu/bcftools-merge
# Create input file `samples.json`
touch samples.json
# Submit your job
choppy batch YaqingLiu/bcftools-merge-latest samples.json -p project_name

Input File

Input file samples.json should be in the form of json. For example:

{
	"vcf": [
          "oss://choppy-cromwell-result/test-choppy/..._pon.vcf",
          "oss://choppy-cromwell-result/test-choppy/..._pon.vcf",
          "oss://choppy-cromwell-result/test-choppy/..._pon.vcf"
        ],
	"panel_id": "PON_20200923",
	"sample_id": "PON_20200923"
}

PS: sample_id is necessary for Choppy system