Changes between Version 5 and Version 6 of Test imputation pipeline


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Timestamp:
Feb 17, 2012 1:09:43 PM (12 years ago)
Author:
a.kanterakis
Comment:

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  • Test imputation pipeline

    v5 v6  
    33
    44== Datasets ==
     5=== Reference ===
    56The reference dataset has been created from the raw VCF data of 1000 Genomes data.
    67 * Download VCF files from : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521
    … …  
    1415}}}
    1516    * Alternatively we coud have used the 1000 Genomes reference panel in impute2 format (legend and hap files) from the impute2 website: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data
     17
     18=== Study panel ===
     19The 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:
     20 * 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
     21 * Download and install hapgen2: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
     22 * Download the list of SNPs in the Hap550 platform:
    1623The study panel is an artificial genotype dataset. Created by
    17 The study panel is an artificial genotype dataset. Created by
    18 The study panel is an artificial genotype dataset. Created by
    19 The study panel is an artificial genotype dataset. Created by