| 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¶
- --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¶
AUTHOR¶
SHAPEIT4 was written by Olivier Delaneau.
| December 2018 |