Changes between Version 14 and Version 15 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 1:34:58 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v14 v15  
    205205==== Source code ====
    206206http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertListsOfPedAndMapFilesToGenAndSample.py
     207=== UseImpute2WithOnePhasedReferencePanel ===
     208Run impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) with one phased reference panel.
     209
     210==== Parameters ====
     211 * impute2Path: Path of the impute2 tool (example: /Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2)
     212 * mParameter: Fine-scale recombination map for the region to be analyzed. (example: Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt )
     213 * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype (example: /Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps)
     214 * lParameter: Legend file(s) with information about the SNPs in the -h file(s) (example: /Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend)
     215 * gParameter: File containing genotypes for a study cohort that we want to impute: (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.gen)
     216 * startPos: Start position of the genomic interval to use for inference (example: 1)
     217 * endPos: End position of the genomic interval to use for inference (example: 5000000)
     218 * Ne: Effective size' of the population (commonly denoted as Ne in the population genetics literature) from which your dataset was sampled (example: 11418)
     219 * oParameter: Name of main output file. (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.impute2)
     220
     221==== Example ====
     222{{{
     223#!div style="font-size: 80%"
     224Code highlighting:
     225  {{{#!python
     226seImpute2WithOnePhasedReferencePanel(
     227        impute2Path="/Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2",
     228        mParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt",
     229        hParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps",
     230        lParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend",
     231        gParameter="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.gen",
     232        startPos=1,
     233        endPos=5000000,
     234        Ne=11418,
     235        oParameter="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.impute2")
     236  }}}
     237}}}
     238
     239==== Source code ====
     240http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanel.py
    207241== BEABLE pipeline ==
    208242