Changes between Version 12 and Version 13 of Test imputation pipeline


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Timestamp:
Feb 17, 2012 1:54:27 PM (12 years ago)
Author:
a.kanterakis
Comment:

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  • Test imputation pipeline

    v12 v13  
    1717
    1818=== Study panel ===
    19 The study panel is an artificial genotype dataset. The dataset contains the SNPs set of the Illumina Hap550 platform. To generate it we followed the following steps:
     19The study panel is an artificial genotype dataset. It consists of 5000 samples in the SNP set of the Illumina Hap550 platform. To generate it we followed the following steps:
    2020 * Download the genetic map of b37 release of human genome from impute2: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data
    2121 * Download and install hapgen2: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
     
    4141SNPs not in 1000Genomes but in Hap550: 935
    4242}}}
     43
     44== "Amsterdam" Run ==
     45
     46== "Groningen" Run ==
     47 * The first step is to upload the data in the grid.
     48 * Use Molgenis - compute to generate the scripts (jdl and sh files)
     49}}}