filterImputeData: Filter genetic variants

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

Description

Filter genetic variants accoring to the imputation quality score with the help of .impute2_info files generated by IMPUTE2. In this case we keep variants with imputation info score of greater than 0.6.

Usage

filterImputeData(plink, suffix4impute2info, impute2infoFile, infoScore,
  badImputeSNPfile, prefix4imputedPlink, prefix4imputedFilterPlink)

Arguments

plink	an executable PLINK program in either the current working directory or somewhere in the command path.
suffix4impute2info	the suffix of IMPUTE2 generated files that store the imputation quality score for each variant, i.e. .impute2_info files.
impute2infoFile	the output file of impute2 info scores which consists of two columns, namely all imputed SNPs and their info scores. Note that imputed SNPs with more than two alleles are dropped.
infoScore	the cutoff of filtering imputation quality score for each variant.
badImputeSNPfile	the output file of SNPs with bad info scores.
prefix4imputedPlink	the prefix of the final imputed PLINK format files.
prefix4imputedFilterPlink	the prefix of the final imputed and filtered PLINK format files.

Value

The filtered PLINK format imputed files, a pure text file with all removed SNPs (with bad infoScore) and a pure text file with the info scores of all imputed SNPs that has two columns: the SNPs and the corresponding info scores.

Author(s)

Junfang Chen <[e-mail]>

Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.