Changes between Initial Version and Version 1 of generateArtificialGwas


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Timestamp:
2012-09-06T13:26:57+02:00 (13 years ago)
Author:
Patrick
Comment:

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  • generateArtificialGwas

    v1 v1  
     1This page describes how to create random GWAS data for plink. A fake phenotype is generated for which significantly associated SNPs are present in the data.
     2
     3= Required tools =
     4 * Gtool (http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html)
     5 * Hapgen2 (!https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html)
     6 * Plink (http://pngu.mgh.harvard.edu/~purcell/plink/)
     7
     8= Required data =
     9Genotypes on which generated data is based. For instance: https://mathgen.stats.ox.ac.uk/impute/impute_v1.html#Using_IMPUTE_with_the_HapMap_Data
     10
     11= Procedure =
     12For this analysis we used the hapmap data:
     13
     14 * Genotype data: !https://mathgen.stats.ox.ac.uk/wtccc-software/rel24_poly/haplotype+legend_files_CEU_r24.tgz
     15
     16== Generate the artificial GWAS data ==
     17{{{
     18hapgen2 -h hapmap_r24_b36_fwd.consensus.qc.poly.chr22_ceu.phased -l chr22.ceu.r24.legend -m genetic_map_chr22_CEU_b36.txt -o test -dl 14431347 0 2 10 -n 2000 2000
     19}}}