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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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reproducible results across different platforms, eg. linux and mac #159

Closed shajoezhu closed 7 years ago

shajoezhu commented 7 years ago

Ubuntu

joezhu@joezhu-M3800:~/DEploid$ ./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -noPanel -seed 1 MCMC step 100% completed. #########################################

dEploid v0.3-beta.1 log

######################################### Program was compiled on: Wed-23-Nov-21:12:16-UTC-2016 dEploid version: bfc23824f00f25aee2d31762201b32e6516b6ea5

Input data: Panel: PLAF: data/testData/labStrains.test.PLAF.txt VCF: data/testData/PG0390-C.test.vcf

MCMC parameters: MCMC burn: 0.5 MCMC sample: 800 MCMC sample rate: 5 Random seed: 1 Update Prop: YES Update Single: YES Update Pair: YES

Other parameters: Miss copy prob: 0.01 Avrg Cent Morgan: 15000 Ne: 10

Run time: Start at: Wed Nov 23 21:24:24 2016 End at: Wed Nov 23 21:24:27 2016

Output saved to: Likelihood: PG0390-CNopanel.llk Proportions: PG0390-CNopanel.prop Haplotypes: PG0390-CNopanel.hap

Proportions at the last iteration: 0.79083 0.000128917 0.208823 9.58858e-05 0.000121799

shajoezhu commented 7 years ago

Mac

dhcp185:DEploid joezhu$ ./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -noPanel -seed 1 MCMC step 100% completed. #########################################

dEploid v0.3-beta.1 log

######################################### Program was compiled on: Wed-23-Nov-2016-21:24:39-UTC dEploid version: bfc23824f00f25aee2d31762201b32e6516b6ea5

Input data: Panel: PLAF: data/testData/labStrains.test.PLAF.txt VCF: data/testData/PG0390-C.test.vcf

MCMC parameters: MCMC burn: 0.5 MCMC sample: 800 MCMC sample rate: 5 Random seed: 1 Update Prop: YES Update Single: YES Update Pair: YES

Other parameters: Miss copy prob: 0.01 Avrg Cent Morgan: 15000 Ne: 10

Run time: Start at: Wed Nov 23 21:24:46 2016 End at: Wed Nov 23 21:24:50 2016

Output saved to: Likelihood: PG0390-CNopanel.llk Proportions: PG0390-CNopanel.prop Haplotypes: PG0390-CNopanel.hap

Proportions at the last iteration: 0.79083 0.000128917 0.208823 9.58858e-05 0.000121799

shajoezhu commented 7 years ago

closed by #162