Man pages for Junfang/Gimpute
Gimpute: An efficient genetic data processing and imputation pipeline
| changedXyChr | Split chromosome X into pseudoautosomal region and... |
| chrWiseSplit | Split genome-wide genotyping data into separate files by... |
| chunk4eachChr | Chunk each chromosome into multiple segments |
| filterImputeData | Filter genetic variants |
| formatConvertGtool | Convert IMPUTE2 format files into PLINK format |
| imputedByImpute2 | Impute genotypes using IMPUTE2 |
| mergeImputeData | Merge chunk-wise PLINK files |
| plotPCA4plink | Population outlier detection via PCA |
| prepareChipAnnoFile4affymetrix | prepare Affymetrix chip annotation file |
| prepareChipAnnoFile4Illumina | prepare Illumina chip annotation file |
| prePhasingByShapeit | Prephasing genotypes using SHAPEIT |
| removedDoubleProbes | Remove duplicated probes or SNPs |
| removedExclProbe | Remove probes or SNPs |
| removedInstFhet | Remove subjects with great autosomal heterozygosity deviation |
| removedInstMiss | Remove subjects with missing values |
| removedMaleHetX | Remove male subjects with haploid heterozygous SNPs |
| removedMonoSnp | Remove monomorphic SNPs |
| removedParentIdsMiss | Reset paternal and maternal codes |
| removedSnpFemaleChrXhweAll | Hardy weinberg equilibrium test for chromosome X SNPs in... |
| removedSnpFemaleChrXhweControl | Hardy weinberg equilibrium test for chromosome X SNPs in... |
| removedSnpFemaleChrXmiss | remove chromosome X SNPs in females |
| removedSnpHetX | Remove heterozygous SNPs in haploid male chromosome X |
| removedSnpHWEautoControl | Hardy weinberg equilibrium test for autosomal SNPs in... |
| removedSnpMiss | Remove SNPs with missing values |
| removedSnpMissDiff | Remove SNPs with difference in SNP missingness between cases... |
| removedSnpMissPostImp | Remove SNPs after post imputation |
| removedUnmapProbes | Remove unmapped probes or SNPs |
| removeDupID | Remove duplicated sample IDs |
| removedWrongAnceInst | Remove samples with improper ancestry |
| removedYMtSnp | Remove SNPs on the chromosome Y and mitochondria |
| removeNoGroupId | Remove samples without group information |
| removeOutlierByPCs | Remove population outliers by principle components |
| renamedSnpChr | Remaming chromosomes |
| replaceGroupId | Replace group and geneder presentation into proper PLINK... |
| setHeteroHaploMissing | Set haploid heterozygous SNPs as missing |
| updatedSnpInfo | Update the probes or SNPs information |
