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)