Changes between Version 15 and Version 16 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 1:55:19 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v15 v16  
    239239==== Source code ====
    240240http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanel.py
     241
     242=== UseImpute2ToImputeBedBimFamFilesWithOnePhasedReferencePanel ===
     243Use 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
    241258== BEABLE pipeline ==
    242259