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Matthew Porter edited this page Sep 23, 2013 · 20 revisions
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DupHMM: An easy to use copy number variant identifier


  1. Introduction
  2. Installation
  3. Running DupHMM

DupHMM was developed by Matthew Porter, a Korf Lab member at the University of California, Davis. DupHMM is being provided under the MIT open source license.

The development of DupHMM is being continued under the KorfLab GitHub repository "Ploidamatic". Reliance on the Poisson for emission probabilities has been forgone in the new edition for emission probabilities based on a normal fit, and additional 'high' and 'low' HMM states have been connected to each CNV state to account for anomalous coverage, typically mismapping induced, which cause transient coverage dips and spikes.

If you encounter any bugs or have any questions or suggestions, feel free to contact me at mdporter@ucdavis.edu