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SHAPEIT4(1) General Commands Manual SHAPEIT4(1)

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


Produce help message
Seed of the random number generator
Number of thread used

Input files

Genotypes to be phased in VCF/BCF format
Reference panel of haplotypes in VCF/BCF format
Scaffold of haplotypes in VCF/BCF format
Genetic map
Target region
Informs phasing using PS field from read based phasing

MCMC parameters

Iteration scheme of the MCMC
Pruning threshold
Store K sizes in last iterations

PBWT parameters

Do not initialise haplotypes by PBWT (rephase input haplotype data)
Storage frequency of PBWT indexes in variant numbers (i.e. 16 means storage every 16 variants)
Depth of PBWT indexes to condition on

HMM parameters

Minimal size of the phasing window
Effective size of the population

Output files

Phased haplotypes in VCF/BCF format
Log file

SEE ALSO

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

AUTHOR

SHAPEIT4 was written by Olivier Delaneau.

December 2018