
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)
