dot-filterImputeData: Filter genetic variants

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

Filter genetic variants

Description

Filter out genetic variants accoring to the imputation quality score.

Usage

.filterImputeData(
  plink,
  suffix4impute2info,
  outputInfoFile,
  infoScore = 0.6,
  inputPrefix,
  outputPrefix
)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
suffix4impute2info	the suffix of input IMPUTE2 generated files that store the imputation quality score for each variant from .impute2_info files.
outputInfoFile	the output file of impute2 info scores consisting of two columns: all imputed SNPs and their info scores.
infoScore	the cutoff of filtering imputation quality score for each variant. The default value is 0.6.
inputPrefix	the prefix of the input imputed PLINK binary files.
outputPrefix	the prefix of the output filtered PLINK binary files.

Details

Filter genetic variants accoring to the imputation quality score with the help of .impute2_info files generated by IMPUTE2. Often, we keep variants with imputation info score of greater than 0.6. Note that imputed SNPs with more than two alleles are not considered.

Value

A pure text file contains the info scores of all imputed SNPs with two columns: SNP names and the corresponding info scores. A pure text file with all excluded SNPs having bad info scores. The filtered PLINK binary imputed files.

Author(s)

Junfang Chen

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