Man pages for transbioZI/Gimpute
Gimpute: An efficient genetic data processing and imputation pipeline
| checkAlign2ref | Check the alignment with the imputation reference panel |
| chrWiseSplit | Split genome-wide genotyping data into chromosome-wide PLINK... |
| chunk4eachChr | Chunk each chromosome into multiple segments |
| computeInfoByQctool | Calculate the info score by QCTOOL |
| dot-convertImpute2ByGtool | Convert IMPUTE2 format files into PLINK format |
| dot-filterImputeData | Filter genetic variants |
| dot-filterImputeData2 | Filter genetic variants |
| dot-getInfoScoreImpute2 | Extract info score |
| dot-imputedByImpute2 | Impute genotypes using IMPUTE2 |
| dot-imputedByImpute4 | Impute genotypes using IMPUTE4 |
| dot-mergePlinkData | Merge chunk-wise PLINK files |
| dot-prepareLegend2bim | Prepare a bim-like reference file |
| dot-prePhasingByShapeit | Prephasing genotypes using SHAPEIT |
| dot-snpSharedPos | Find shared genomic position between two files. |
| extractByGenipe | Extract imputed markers using Genipe |
| genoQC | Quality control for genotype data |
| getGroupLabel | Get the outcome label of the genotype data |
| imputedByGenipe | Impute genotypes using Genipe |
| mergeByGenipe | Merge imputed files using Genipe |
| phaseImpute | Phasing and imputation |
| plotPCA4plink | Population outlier detection |
| postImpQC | Post imputation quality control |
| prepareAnnoFile4affy | prepare Affymetrix chip annotation file |
| reductExpand | Post imputation data extraction and expansion |
| removedDoubleProbes | Remove duplicated SNPs |
| removedExclProbe | Remove improper SNPs |
| removedInstFhet | Remove subjects with abnormal autosomal heterozygosity... |
| removedInstMiss | Remove subjects with missing values |
| removedMaleHetX | Remove male subjects with haploid heterozygous SNPs |
| removedMendelErr | Check Mendel errors for family-based data |
| removedMonoSnp | Exclude monomorphic SNPs |
| removedParentIdsMiss | Reset paternal and maternal codes |
| removedSnpFemaleChrXhweControl | Hardy Weinberg Equilibrium test for chromosome X SNPs in... |
| removedSnpFemaleChrXmiss | remove chromosome X SNPs in females |
| removedSnpHetX | Remove heterozygous SNPs in male chromosome X |
| removedSnpHWEauto | Hardy Weinberg Equilibrium test for autosomal SNPs |
| removedSnpMiss | Remove SNPs with missing values |
| removedSnpMissDiff | Remove SNPs with difference in SNP missingness between cases... |
| removedSnpMissPostImp | Remove SNPs after post imputation |
| removedUnmapProbes | Remove SNPs not in the chip annotation file |
| removedWrongAnceInst | Remove samples with incorrect ancestry |
| removedYMtSnp | Remove SNPs on the chromosome Y and mitochondrial DNA |
| removeNoGroupId | Remove samples without group information |
| removeOutlierByPCs | Remove population outliers |
| removeSampID | Remove samples in PLINK files |
| renamePlinkBFile | Rename PLINK binary files |
| setHeteroHaploMissing | Set haploid heterozygous SNPs as missing |
| splitXchr | Split chromosome X into pseudoautosomal region and... |
| updatedSnpInfo | Update the SNP information |
| updateGenoInfo | Update genotype information |
| updateGroupIdAndSex | Update group and geneder information |
