| | 241 | |
| | 242 | === UseImpute2ToImputeBedBimFamFilesWithOnePhasedReferencePanel === |
| | 243 | Use impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) to impute Bed Bim Fam Files with one phased reference panel. |
| | 244 | |
| | 245 | ==== Parameters ==== |
| | 246 | * plink_path: Path to plink executable (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink) |
| | 247 | * bbf_path: Path to BED, BIM, FAM file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05) |
| | 248 | * ped_path: Filename of exported PED file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped) |
| | 249 | * map_path: Filename of exported MAP file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map) |
| | 250 | * output_divided_path: Directory where the divided according to chromosomes Pem and Map files will be exported (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes) |
| | 251 | * suffix: Suffix of the exported files (example: output_) |
| | 252 | * gtoolPath: Path of gtool (example: /Users/alexandroskanterakis/Tools/gtool/gtool) |
| | 253 | * impute2Path: Path of impute2: (example: /Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2) |
| | 254 | * mParameter: Fine-scale recombination map for the region to be analyzed |
| | 255 | * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype |
| | 256 | * lParameter: Legend file(s) with information about the SNPs in the -h file(s) |
| | 257 | |
