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NCBI-Hackathons / Scan2CNV

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PennCNV HMM file #17

Closed ekarlins closed 7 years ago

ekarlins commented 7 years ago

Do we need to create an HMM file?

See PennCNV documentation to figure this out, and if so put code to generate this in "scripts" dir.

mtbrown22 commented 7 years ago

Looks like the HMM file is bundled with PennCNV. We just need to provide the signal intensity files in proper format.

See first paragraph here

ekarlins commented 7 years ago

@mtbrown22, I think you are right about the HMM file. That first paragraph is confusing, though. It also says the PFB and GC Model file are part of the bundle. Though there are example files for those, the PFB is specific to the array and the GC Model file is specific for the genome build. So those two really need to be generated. I think the HMM will work, though.