NAME

       shapeit4 - fast and accurate method for estimation of haplotypes (phasing)

SYNOPSIS

       shapeit4 [options]

DESCRIPTION

       Segmented  HAPlotype  Estimation and Imputation Tools version 4 (SHAPEIT4).  SHAPEIT4 is a
       fast and accurate method for estimation of haplotypes (aka  phasing)  for  SNP  array  and
       sequencing  data.  It includes a Positional Burrow Wheeler Transform (PBWT) based approach
       to quickly select a small set of informative  conditioning  haplotypes  to  be  used  when
       updating  the  phase of an individual.  It accounts for sets of pre-phased genotypes (i.e.
       haplotype scaffold).  The scaffold can  be  derived  either  from  family  data  or  large
       reference  panels.   It  reads and writes files using HTSlib for better I/O performance in
       either VCF or BCF formats.  The genotype graph and HMM routines have  been  re-implemented
       for better hardware usage and performance.

OPTIONS

   Basic options
       --help
              Produce help message

       --seed arg (=15052011)
              Seed of the random number generator

       -T, --thread arg (=1)
              Number of thread used

   Input files
       -I, --input arg
              Genotypes to be phased in VCF/BCF format

       -H, --reference arg
              Reference panel of haplotypes in VCF/BCF format

       -S, --scaffold arg
              Scaffold of haplotypes in VCF/BCF format

       -M, --map arg
              Genetic map

       -R, --region arg
              Target region

       --use-PS arg
              Informs phasing using PS field from read based phasing

   MCMC parameters
       --mcmc-iterations arg (=5b,1p,1b,1p,1b,1p,5m)
              Iteration scheme of the MCMC

       --mcmc-prune arg (=0.999)
              Pruning threshold

       --mcmc-store-K arg
              Store K sizes in last iterations

   PBWT parameters
       --pbwt-disable-init
              Do not initialise haplotypes by PBWT (rephase input haplotype data)

       --pbwt-modulo arg (=8)
              Storage  frequency  of PBWT indexes in variant numbers (i.e. 16 means storage every
              16 variants)

       --pbwt-depth arg (=4)
              Depth of PBWT indexes to condition on

   HMM parameters
       -W, --window arg (=2000000)
              Minimal size of the phasing window

       --effective-size arg (=15000)
              Effective size of the population

   Output files
       -O, --output arg
              Phased haplotypes in VCF/BCF format

       --log arg
              Log file

SEE ALSO

       https://odelaneau.github.io/shapeit4/

AUTHOR

       SHAPEIT4 was written by Olivier Delaneau.

                                          December 2018                               SHAPEIT4(1)