Is your feature request related to a problem? Please describe
Currently the cnvkit/reference module only seems to support generating a flat reference as you cannot provide coverage files to generate a pooled normal reference e.g
cnvkit.py reference normal1_coverage.cnn normal2coverage.cnn ... -f hg38.fa -o reference.cnn
Describe the solution you'd like
The module should be extended by adding an input for the normal-sample coverage .cnn files and passing those files positionally to cnvkit.py reference. That is the mechanism CNVkit itself uses to distinguish a pooled reference from a flat reference. The current module only supplies --fasta, --targets, and --antitargets, so CNVkit has no normal coverage profiles to pool and therefore builds a flat reference.
Describe alternatives you've considered
No response
Additional context
No response
Is your feature request related to a problem? Please describe
Currently the
cnvkit/referencemodule only seems to support generating a flat reference as you cannot provide coverage files to generate a pooled normal reference e.gDescribe the solution you'd like
The module should be extended by adding an input for the normal-sample coverage .cnn files and passing those files positionally to cnvkit.py reference. That is the mechanism CNVkit itself uses to distinguish a pooled reference from a flat reference. The current module only supplies --fasta, --targets, and --antitargets, so CNVkit has no normal coverage profiles to pool and therefore builds a flat reference.
Describe alternatives you've considered
No response
Additional context
No response