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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Prototype siHMM. #2985

Closed droazen closed 6 years ago

droazen commented 7 years ago

@samuelklee commented on Fri May 12 2017

Hooking up a siHMM (or some variation) to the coverage model from https://github.com/broadinstitute/gatk-protected/issues/1038 will be our first cut at GATK CNV 2.0. Performance and convergence on WGS-size data should be a priority. The end goal will be a joint siHMM once we also have the 2.0 allele-fraction model prototyped.

samuelklee commented 6 years ago

I think this is obviated by kernel segmentation. We may use some sort of HMM for the tumor heterogeneity tool, but we can open new, more relevant issues then.