A Nextflow workflow that integrates multiple CNV callers for improved CNV calling from exome sequencing data.
The approach uses the following exome sequencing-based CNV callers:
- CANOES': https://github.com/ShenLab/CANOES
- CLAMMS: https://github.com/rgcgithub/clamms
- XHMM: https://zzz.bwh.harvard.edu/xhmm/
The workflow includes CNV calling, merging and random forest validation steps.
For the CNV calling step alone and including an additional tool (INDELLIBLE: https://github.com/HurlesGroupSanger/indelible), you can type git clone https://github.com/phelelani/nf-exomecnv.git.
This project is a collaboration of Phelelani Mpangase and Yoni Wolberg as part of the DDD-Africa project at the University of the Witwatersrand.