The CNV task currently outputs various text files that are then converted to a 'report' via several hacky steps. It would be ideal to convert the *.segs.txt file to VCF format with a short python/perl script, which can then be combined with the manta VCF and annotated with VEP.
dhspence
commented
5 years ago
The CNV task currently outputs various text files that are then converted to a 'report' via several hacky steps. It would be ideal to convert the *.segs.txt file to VCF format with a short python/perl script, which can then be combined with the manta VCF and annotated with VEP.