imputedByGenipe: Impute genotypes using Genipe

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

Impute genotypes using Genipe

Description

Perform imputation by Genipe for the autosomal and sex chromosome prephased known haplotypes with a reference panel. Note that pre-phasing using SHAPEIT is done without the refernce haplotypes.

Usage

imputedByGenipe(
  chrs,
  impRefDir,
  inputPrefix,
  shapeit,
  impute2,
  plink,
  fastaFile,
  segmentSize,
  thread4impute2,
  thread4shapeit
)

Arguments

chrs	specifiy the chromosomes for imputation. There are four different options ("autosomes", "1, or 2, or 3...or 22", "23", "25"). 1.) 'autosomes': will impute chromosome 1 to 22 together; 2.) 'chrs' belongs to one of (1, 2,...22) then the imputation is done just for one autosomal chromosome. 3.) '23' will do the imputation for the non-pseudoautosomal region of chromosome 23. 4.) '25' imputes for the pseudoautosomal regions of chromosome 23.
impRefDir	the directory where the imputation reference files are located.
inputPrefix	the prefix of the input PLINK binary files.
shapeit	an executable SHAPEIT binary program in either the current working directory or somewhere in the command path.
impute2	an executable IMPUTE2 binary program in either the current working directory or somewhere in the command path.
plink	an executable program in either the current working directory or somewhere in the command path.
fastaFile	the human reference files for the initial strand check.
segmentSize	the length of a single segment for imputation.
thread4impute2	the number of threads for the imputation.
thread4shapeit	the number of threads for phasing.

Value

The imputed files using genipe.

Author(s)

Junfang Chen

References

Lemieux Perreault, L. P., et al. (2016). genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools. Bioinformatics, 32(23), 3661-3663.

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