Man pages for Junfang/Gimpute
Gimpute: An efficient genetic data processing and imputation pipeline

changedXyChrSplit chromosome X into pseudoautosomal region and...
chrWiseSplitSplit genome-wide genotyping data into separate files by...
chunk4eachChrChunk each chromosome into multiple segments
filterImputeDataFilter genetic variants
formatConvertGtoolConvert IMPUTE2 format files into PLINK format
imputedByImpute2Impute genotypes using IMPUTE2
mergeImputeDataMerge chunk-wise PLINK files
plotPCA4plinkPopulation outlier detection via PCA
prepareChipAnnoFile4affymetrixprepare Affymetrix chip annotation file
prepareChipAnnoFile4Illuminaprepare Illumina chip annotation file
prePhasingByShapeitPrephasing genotypes using SHAPEIT
removedDoubleProbesRemove duplicated probes or SNPs
removedExclProbeRemove probes or SNPs
removedInstFhetRemove subjects with great autosomal heterozygosity deviation
removedInstMissRemove subjects with missing values
removedMaleHetXRemove male subjects with haploid heterozygous SNPs
removedMonoSnpRemove monomorphic SNPs
removedParentIdsMissReset paternal and maternal codes
removedSnpFemaleChrXhweAllHardy weinberg equilibrium test for chromosome X SNPs in...
removedSnpFemaleChrXhweControlHardy weinberg equilibrium test for chromosome X SNPs in...
removedSnpFemaleChrXmissremove chromosome X SNPs in females
removedSnpHetXRemove heterozygous SNPs in haploid male chromosome X
removedSnpHWEautoControlHardy weinberg equilibrium test for autosomal SNPs in...
removedSnpMissRemove SNPs with missing values
removedSnpMissDiffRemove SNPs with difference in SNP missingness between cases...
removedSnpMissPostImpRemove SNPs after post imputation
removedUnmapProbesRemove unmapped probes or SNPs
removeDupIDRemove duplicated sample IDs
removedWrongAnceInstRemove samples with improper ancestry
removedYMtSnpRemove SNPs on the chromosome Y and mitochondria
removeNoGroupIdRemove samples without group information
removeOutlierByPCsRemove population outliers by principle components
renamedSnpChrRemaming chromosomes
replaceGroupIdReplace group and geneder presentation into proper PLINK...
setHeteroHaploMissingSet haploid heterozygous SNPs as missing
updatedSnpInfoUpdate the probes or SNPs information
Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.