Workflow for imputation of PNC genomics data (prior to genome wide association study). Details on how we used this workflow contained here: /documentation/Genotype-Imputation.pdf.
Order to run for genotype imputation:
| Filename | Description |
|---|---|
| 00a-createPheno.R | Run as Rscript to make phenotype file with FID and IID as first two columns |
| 00b-createFID_IID.R | Run as Rscript to make FID_IID file |
| 00c-createSexInfo.R | Run as Rscript to make subject sex information file |
| 01a-subsetEA.sh | Submit as PBS job to subset the genotype files for race = EA |
| 01b-recodeAlleles.sh | Submit as PBS job to recode alleles from 12 (AB) coding to ACGT coding |
| 02a-preImputeQc.sh | Submit as PBS job to perform quality checking |
| 02b-alignment_Omni.sh | Submit as PBS job to perform alignment using HRC, run sh Run-plink.sh before moving on |
| 02b-alignment_Quad.sh | Submit as PBS job to perform alignment using HRC, run sh Run-plink.sh before moving on |
| 02b-alignment_v1.sh | Submit as PBS job to perform alignment using HRC, run sh Run-plink.sh before moving on |
| 02b-alignment_v3.sh | Submit as PBS job to perform alignment using HRC, run sh Run-plink.sh before moving on |
| 02c-bgzip.sh | Submit as PBS job to compress chromosome files for upload to imputation server |
| 02e-assayed.sh | Run with: sh 02d-assayed.sh, should complete very quickly, produces assayed.txt |
At this point imputation should be attempted/completed on the Michigan Imputation Server.
| Filename | Description |
|---|---|
| 02d-index.sh | Submit as PBS job to index imputed files after download from imputation server |
| 03a-reheader_Omni.sh | Submit as PBS array job to reheader GO_Omni imputed chromosome files |
| 03b-reheader_Quad.sh | Submit as PBS array job to reheader GO_Quad imputed chromosome files |
| 03c-reheader_v1_hg18.sh | Submit as PBS array job to reheader GO_v1_hg18 imputed chromosome files |
| 03d-reheader_v3.sh | Submit as PBS array job to reheader GO_v3 imputed chromosome files |
| 04-merge.sh | Merge the separate reheadered chip chromosome files into one set of chromosome files |
| 05-final_merge.sh | Merge the separate chromosome files into one single genotype file |
| 06-final_qc.sh | Perform LD pruning, IBD pruning, output cleaned hrc file |
| 07a-convert.sh | Convert from .ped/.map to EIGENSTRAT file format |
| 07b-pca.sh | Perform PCA to extract eigenvectors and eigenvalues |
| 08-filterR2.sh | Use the Rsquared values computed during imputation to remove SNPs with R2 less than 0.8 |
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