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SHAPEIT
* Author : Olivier DELANEAU, University of Lausanne
* Contact : olivier.delaneau@gmail.com
* Version : 4.0.0
* Run date : 07/12/2018 - 13:38:37
Files:
* Input VCF : [unphased.bcf]
* Reference VCF : [reference.bcf]
* Scaffold VCF : [scaffold.bcf]
* Genetic Map : [chr20.b37.gmap.gz]
* Output VCF : [phased.bcf]
* Output LOG : [phased.log]
Parameters:
* Seed : 15052011
* Threads : 4 threads
* MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
* PBWT : Store indexes every 8 variants
* PBWT : Depth of PBWT neighbours to condition on: 4
* HMM : K is variable / min W is 2.00Mb / Ne is 15000
* HMM : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001
Initialization:
* VCF/BCF scanning [Nm=203 / Nr=300 / L=24990 / Reg=20] (0.09s)
* VCF/BCF parsing [Hom=90.0% / Het=10.0% / Pha=2.668%/ / Sca=0.778% / Mis=0.0%] (0.22s)
* GMAP parsing [n=82962] (0.03s)
* cM interpolation [s=3296 / i=21694] (0.63s)
* HAP update (0.02s)
* H2V transpose (0.01s)
* IBD2 mask [l=16662 / n=0] (0.02s)
* PBWT phase sweep (0.19s)
* Build genotype graphs [seg=164449] (0.02s)
Burn-in iteration [1/5]
* V2H transpose (0.00s)
* PBWT selection (0.06s)
* C2H transpose (0.00s)
* HMM computations [K=712.9+/-44.9 / W=3.00Mb] (14.93s)
* HAP update (0.01s)
* H2V transpose (0.00s)
Burn-in iteration [2/5]
* V2H transpose (0.00s)
* PBWT selection (0.06s)
* C2H transpose (0.00s)
* HMM computations [K=658.7+/-50.0 / W=3.00Mb] (13.76s)
* HAP update (0.01s)
* H2V transpose (0.00s)
Burn-in iteration [3/5]
* V2H transpose (0.00s)
* PBWT selection (0.06s)
* C2H transpose (0.00s)
* HMM computations [K=650.4+/-50.9 / W=3.00Mb] (13.65s)
* HAP update (0.01s)
* H2V transpose (0.00s)
Burn-in iteration [4/5]
* V2H transpose (0.00s)
* PBWT selection (0.06s)
* C2H transpose (0.00s)
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