dot-imputedByImpute2: Impute genotypes using IMPUTE2

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

Impute genotypes using IMPUTE2

Description

Perform imputation by IMPUTE2 for the autosomal and sex chromosome prephased known haplotypes with a reference panel.

Usage

.imputedByImpute2(
  impute2,
  chrs,
  prefixChunk,
  phaseDIR,
  referencePanel,
  impRefDIR,
  imputedDIR,
  prefix4eachChr,
  nCore,
  effectiveSize = 20000
)

Arguments

impute2	an executable program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosome codes for imputation.
prefixChunk	the prefix of the chunk files for each chromosome, along with the proper location directory.
phaseDIR	the directory where prephased haplotypes are located.
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.
imputedDIR	the directory where imputed files will be located.
prefix4eachChr	the prefix of IMPUTE2 files for each chunk.
nCore	the number of cores used for computation.
effectiveSize	this parameter controls the effective population size. Commonly denoted as Ne. A universal -Ne value of 20000 is suggested.

Details

If ChrX is available then it is done automatically by passing the flag –chrX to IMPUTE2.

Value

The imputed files for all chunks from the given chromosomes.

Author(s)

Junfang Chen

See Also

phaseImpute2.

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