There are two separate steps, each with their own script, docker image, and CWL tool:
- Process VCF
- Parse VCF
The first step calls SOBDetector on a VCF file. The
second step parses the resulting VCF file and writes to the FILTER field of calls marked as artifacts.
Docker images: mwyczalkowski/ffpe_filter_process:20211216 and mwyczalkowski/ffpe_filter_parse:20211216
Contact: Matt Wyczalkowski ([email protected])