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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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Improve ibd #233

Closed shajoezhu closed 7 years ago

shajoezhu commented 7 years ago
  1. Set default IBD sigma to 20
  2. Compute recombination probabilities, instead of using constant 0.01, which can also be set to const using the flag -recomb
  3. Integrate the IBD state probabilities
  4. Export the IBD state probabilities.
shajoezhu commented 7 years ago

setting sigma to 20 for ibd works well

eff_k_both.pdf

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 92.677% when pulling b8bb4e19571722f9a0dca1a3e5246a17b3f4dbd5 on improveIBD into ee50d4d1a94337126577063522f956ca02fe376e on master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 92.677% when pulling b8bb4e19571722f9a0dca1a3e5246a17b3f4dbd5 on improveIBD into ee50d4d1a94337126577063522f956ca02fe376e on master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 92.677% when pulling 67948c3002e8e56f76df6cac07e258062cb9d9ea on improveIBD into ee50d4d1a94337126577063522f956ca02fe376e on master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.2%) to 92.677% when pulling 67948c3002e8e56f76df6cac07e258062cb9d9ea on improveIBD into ee50d4d1a94337126577063522f956ca02fe376e on master.