| 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. |
| | 242 | === UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches === |
| | 243 | Run impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) with one phased reference panel. Divide the chromosome in batches. |
| | 244 | |
| | 245 | ==== Parameters ==== |
| | 246 | * impute2Path: Path of impute2 (example: /Users/alex/Tools/impute2/impute_v2.1.2_MacOSX_Intel/impute2) |
| | 247 | * mParameter: Fine-scale recombination map for the region to be analyzed (-m parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt) |
| | 248 | * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype (-h parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps) |
| | 249 | * lParameter: Legend file(s) with information about the SNPs in the -h file(s) (-l parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend) |
| | 250 | * gParameter: File containing genotypes for a study cohort that we want to impute (-g parameter) (example: /Volumes/Data2/Impute/alex/gen_sample/chr1.gen) |
| | 251 | * sizeOfBatch: Size of each batch (example: 5000000) |
| | 252 | * Ne: Effective size of the population (commonly denoted as Ne in the population genetics literature) from which your dataset was sampled (example: 11418) |
| | 253 | * oParameter: Name of main output file (-o parameter) (example: /Volumes/Data2/Impute/alex/gen_sample/) |
| | 254 | * suffix: suffix for output fil (example: chr_1_) |
| | 255 | * indexOfChromosome: Chromosome (1-22, X, Y, M) (example: 1) |
