mergeByGenipe: Merge imputed files using Genipe

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

Merge imputed files using Genipe

Description

Concatenate IMPUTE2 output files and retrieve some statistics. This is automatically called by the main genipe pipeline to merge IMPUTE2 files generated for all the genomic segments. For details, see Genipe IMPUTE2 merger options.

Usage

mergeByGenipe(
  inputImpute2,
  chr,
  probability,
  completionRate,
  info,
  outputPrefix
)

Arguments

inputImpute2	the output from IMPUTE2.
chr	specifiy the chromosome segment to be merged, on which the imputation was made.
probability	the probability threshold for no calls. [<0.9]
completionRate	the completion rate threshold for site exclusion. [<0.98]
info	the measure of the observed statistical information associated with the allele frequency estimate threshold for site exclusion. (<0.00)
outputPrefix	the prefix for the imputed output files.

Value

The merged 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.