---
name: "shapeit4"
section: "1"
platform: "linux"
package: "shapeit4"
version: "4.2.2+dfsg-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/shapeit4"
---

# shapeit4(1)

fast and accurate method for estimation of haplotypes (phasing)

## 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.