extractByGenipe: Extract imputed markers using Genipe

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

Extract imputed markers using Genipe

Description

Extract imputed markers located in a specific genomic region using Genipe. Note that, 1.) 'bed' PLINK binary format is specifically used for the output format. 2.) The markers of the whole chromosome are extracted together. For the filtering of maf and info will be done during post imputation.

Usage

extractByGenipe(inputImpute2, inputMAP, outputPrefix, format, prob)

Arguments

inputImpute2	the output from IMPUTE2.
inputMAP	the output PLINK MAP file from Genipe, which will be used for generating markers in a text file (only one column without column name).
outputPrefix	the prefix of the output files. [impute2_extractor]
format	the output format. Can specify either "impute2" for probabilities (same as impute2 format, i.e. 3 values per sample), "dosage" for dosage values (one value between 0 and 2 by sample), "calls" for hard calls, or "bed" for Plink binary format (with hard calls). [impute2]
prob	the probability threshold used when creating a file in the dosage or call format. [0.9]

Value

The extracted 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.