Changes between Version 17 and Version 18 of ImputationPipeline


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Timestamp:
Nov 23, 2010 2:21:45 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v17 v18  
    255255 * indexOfChromosome: Chromosome (1-22, X, Y, M) (example: 1)
    256256
    257 ==== Parameters ====
    258  * plink_path: Path to plink executable (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink)
    259  * bbf_path: Path to BED, BIM, FAM file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05)
    260  * ped_path: Filename of exported PED file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped)
    261  * map_path: Filename of exported MAP file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map)
    262  * output_divided_path: Directory where the divided according to chromosomes Pem and Map files will be exported (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes)
    263  * suffix: Suffix of the exported files (example: output_)
    264  * gtoolPath: Path of gtool (example: /Users/alexandroskanterakis/Tools/gtool/gtool)
    265  * impute2Path: Path of impute2: (example: /Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2)
    266  * mParameter: Fine-scale recombination map for the region to be analyzed
    267  * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype
    268  * lParameter: Legend file(s) with information about the SNPs in the -h file(s)
    269 
     257==== Example ====
     258{{{
     259#!div style="font-size: 80%"
     260Code highlighting:
     261  {{{#!python
     262UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches(
     263        impute2Path = "/Users/alex/Tools/impute2/impute_v2.1.2_MacOSX_Intel/impute2" ,
     264        mParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt" ,
     265        hParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps" ,
     266        lParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend" ,
     267        gParameter = "/Volumes/Data2/Impute/alex/gen_sample/chr1.gen" ,
     268        sizeOfBatch = 5000000 ,
     269        Ne = 11418 ,
     270        oParameter = "/Volumes/Data2/Impute/alex/gen_sample/" ,
     271        suffix = "chr_1_" ,
     272        indexOfChromosome = "1")
     273  }}}
     274}}}
     275
     276==== Source Code ====
     277http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches.py
    270278== BEABLE pipeline ==
    271279