This is the initial release of a pipeline that can take VCF files and converts them to MAF format.
Some further convenience features are available:
- Filtering the variant calls that have a
PASSfilter - Filtering variants that are within regions provided by a bed file
- Liftover variants between genome builds
Some caveats:
- Only VEP annotated VCF files are supported at the moment
- This pipeline was tested on Strelka2, Manta, and Mutect2 VEP-annotated VCF files generated with nf-core/sarek
Full Changelog: https://github.com/qbic-pipelines/vcftomaf/commits/1.0.0