prePhasingByShapeit: Prephasing genotypes using SHAPEIT

In Junfang/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline

Description

Perform prephasing for study genotypes by SHAPEIT for the autosomal and sex chromosome haplotypes using a reference panel (pre-set). If ChrX is available then it is done differently by passing the flag –chrX to SHAPEIT.

Usage

prePhasingByShapeit(shapeit, chrs, dataDIR, prefix4plinkEachChr, impRefDIR,
  phaseDIR, nThread, effectiveSize, nCore)

Arguments

shapeit	an executable SHAPEIT program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosomes for phasing.
dataDIR	the directory where genotype PLINK files are located.
prefix4plinkEachChr	the prefix of PLINK files for each chromosome.
impRefDIR	the directory where the imputation reference files are located.
phaseDIR	the directory where resulting pre-phased files will be located.
nThread	the number of threads used for computation.
effectiveSize	this parameter controls the effective population size.
nCore	the number of cores used for computation. This can be tuned along with nThread.

Value

The pre-phased haplotypes for given chromosomes.

Author(s)

Junfang Chen <[e-mail]>

Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.