Hi,
I found minor error on sample script from link - cnvkit — Clara Parabricks v3.7 documentation
Sample script:
$ pbrun cnvkit
–ref Ref/Homo_sapiens_assembly38.fasta
–in-bam mark_dups_gpu.bam
–out-file output.vcf
The option --out-file does not exist. The correct one is ‘–output-dir’.