Changes between Version 9 and Version 10 of Test imputation pipeline


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Timestamp:
Feb 17, 2012 1:40:21 PM (13 years ago)
Author:
a.kanterakis
Comment:

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  • Test imputation pipeline

    v9 v10  
    2424   * From the Table combo box select: snpArrayIllumina550
    2525   * Click the "get output" button
    26  * For the hapgen2 to run we need to specify at least one causal SNP. We selected the first SNP of the dataset (in our case 16539175). In order to not add
     26 * For the hapgen2 to run we need to specify at least one causal SNP. We selected the first SNP of the dataset (in our case 16539175). In order not to add any genome wide variation in this SNP determine the odds ratio as 1.0:
    2727{{{
    2828hapgen2 \
    … …  
    3535}}}
    3636The study panel is an artificial genotype dataset. Created by
     37    * This command requires 80G of memory.
     38 * Filter the generated gen files with the SNPs from the hap550 file.  According to the documentation of hapgen2 you can specify a list of SNPs and limit the generation of the files in these SNPs (the -t option). I didn't use this option and I filtered the generated data afterwards to the positions of hap550 in order to check if the positions indeed matched. Some stats:
     39{{{
     40SNPs in 1000Genomes and in Hap550: 546,233
     41SNPs in 1000Genomes but not in Hap550: 36,265,509
     42SNPs not in 1000Genomes but in Hap550: 935
     43}}}
    3744The study panel is an artificial genotype dataset. Created by
    38 The study panel is an artificial genotype dataset. Created by
    39 The study panel is an artificial genotype dataset. Created by