formatConvertGtool: Convert IMPUTE2 format files into PLINK format

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

Description

Convert all chunks of IMPUTE2 format files into PLINK format using GTOOL.

Usage

formatConvertGtool(gtool, chrs, prefixChunk, phaseDIR, imputedDIR,
  prefix4plinkEachChr, suffix4imputed, postImputeDIR, nCore)

Arguments

gtool	an executable GTOOL program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosomes for conversion
prefixChunk	the prefix of the chunk files for each chromosome, along with the proper location directory.
phaseDIR	the directory where pre-phased files are located.
imputedDIR	the directory where the imputated files are located.
prefix4plinkEachChr	the prefix of the input IMPUTE2 files and also the output PLINK files for each chunk.
suffix4imputed	the suffix of the IMPUTE2 format file that stores the imputed value.
postImputeDIR	the directory where converted PLINK files will be located.
nCore	the number of cores used for computation.

Value

The converted PLINK format files for each chunk.

Author(s)

Junfang Chen <[e-mail]>

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