dot-convertImpute2ByGtool: Convert IMPUTE2 format files into PLINK format

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

Convert IMPUTE2 format files into PLINK format

Description

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

Usage

.convertImpute2ByGtool(
  gtool,
  chrs,
  prefixChunk,
  phaseDIR,
  imputedDIR,
  prefix4eachChr,
  suffix4imputed,
  postImputeDIR,
  threshold,
  SNP = TRUE,
  nCore
)

Arguments

gtool	an executable program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosome codes for conversion.
prefixChunk	the prefix of the chunk files for each chromosome, along with the location directory.
phaseDIR	the directory where pre-phased files are located.
imputedDIR	the directory where the imputated files are located.
prefix4eachChr	the prefix of the input IMPUTE2 files and also the output PLINK binary files for each chunk.
suffix4imputed	the suffix of the IMPUTE2 format file that stores the imputed value. Both ".impute2" and ".gen" are accepted.
postImputeDIR	the directory where converted PLINK binary files will be located.
threshold	threshold for merging genotypes from GEN probability. Default 0.9.
SNP	A logical value indicating if the data is entirely comprised single nucleotide polymorphisms then it can be set as TRUE and the genotypes are expressed as pairs of A,C,G,T and unknowns are represented as N N.
nCore	the number of cores used for computation.

Value

The converted binary PLINK format files for each chunk from IMPUTE2 results.

Author(s)

Junfang Chen

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