dot-prePhasingByShapeit: Prephasing genotypes using SHAPEIT

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

Prephasing genotypes using SHAPEIT

Description

Perform prephasing for study genotypes by SHAPEIT for the autosomal and sex chromosome haplotypes using a reference panel (pre-set).

Usage

.prePhasingByShapeit(
  shapeit,
  chrs,
  dataDIR,
  prefix4eachChr,
  referencePanel,
  impRefDIR,
  phaseDIR,
  nThread = 40,
  effectiveSize = 20000,
  nCore = 1
)

Arguments

shapeit	an executable program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosome codes for phasing.
dataDIR	the directory where genotype PLINK binary files are located.
prefix4eachChr	the prefix of PLINK binary files for each chromosome.
referencePanel	a string indicating the type of imputation reference panels is used: c("1000Gphase1v3_macGT1", "1000Gphase3").
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. The default value is 40.
effectiveSize	this parameter controls the effective population size. The default value is 20000.
nCore	the number of cores used for computation. This can be tuned along with nThread. The default value is 1.

Details

If ChrX is available then it is done automatically by passing the flag –chrX to SHAPEIT.

Value

The pre-phased haplotypes for given chromosomes.

Author(s)

Junfang Chen

See Also

phaseImpute2.

transbioZI/Gimpute documentation built on April 10, 2022, 4:20 a.m.