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-Gene Expression 
-
-Input files 
-
-```
---g | --gexp                   set gene expression file
---p | --pmap                   set the genecode gtf file
---tmpt                         set the temporary file directory
---rest                         set the result file directory
-
-
-Temporary files
-
-name                        
-
-gexp                         
-
-Result files
-
-gene_name             File with name for all the genes
-
-gene_pos              File with the physical location for all the genes
-
-gene_gexp             File with the gene expression after preprocessing
-
-gexpID                File with the ID for genes left after preprocessing
-```
-
-Genotype 
-
-Input files
-
-```
- --r | --reads                   set the GTEx gene reads file in gct format
- --t | --tpm                     set the gene tpm file
- --g | --gtf                     set the genecode gtf file
-```
-
-```
- --p | --ped                   set ped file
- --m | --map                   set map file
- --mind                        set the missing per individual cutoff
- --geno                        set the missing per markder cutoff
- --hwe                         set Hardy-Weinberg equilibrium cutoff
- --nchr                        set the chromosome number
- --r | --ref                   set the reference file for imputation
- --gmap                        set the genomic map file
- --i | --int                   set the interval length for impute2
- --ncores                      set the number of cores
-```
-
-Temporary files
-
-intermediate ped files 
-
-intermediate map files 
-
-Result files
-
-Genotype.sampleID
-
-Geno
-
-# Adjust for Covariates
-
-Input files 
-
-Temporary files 
-
-Result files