imputedByImpute2: Impute genotypes using IMPUTE2

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

Description

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

Usage

imputedByImpute2(impute2, chrs, prefixChunk, phaseDIR, impRefDIR, imputedDIR,
  prefix4plinkEachChr, nCore, effectiveSize)

Arguments

impute2	an executable IMPUTE2 program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosomes 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.
impRefDIR	the directory where the imputation reference files are located.
imputedDIR	the directory where imputed files will be located.
prefix4plinkEachChr	the prefix of IMPUTE2 files for each chunk.
nCore	the number of cores used for computation.
effectiveSize	this parameter controls the effective population size.
XPAR	a logical value indicating whether –chrX flag should be passed for prephasing using SHAPEIT. –chrX flag, specifically for chrX imputation'

Value

The imputed files for all chunks from given chromosomes.

Author(s)

Junfang Chen <[e-mail]>

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