shapeit41

Fast and accurate method for estimation of haplotypes (phasing)

Usage

shapeit4 [options]

Overview

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